full wwpdb nmr structure validation report o i - rcsb

Full wwPDB NMR Structure Validation Report iO

May 28, 2020 � 11:51 pm BST

PDB ID : 2MGTTitle : Zinc induced dimer of the metal binding domain 1-16 of human amyloid beta-

peptide with Alzheimer's disease pathogenic English mutation H6RAuthors : Polshakov, V.; Istrate, A.; Kozin, S.

Deposited on : 2013-11-06

This is a Full wwPDB NMR Structure Validation Report for a publicly released PDB entry.

We welcome your comments at [email protected]

A user guide is available athttps://www.wwpdb.org/validation/2017/NMRValidationReportHelp

with speci�c help available everywhere you see the iO symbol.

The following versions of software and data (see references iO) were used in the production of this report:

Cyrange : Kirchner and Güntert (2011)NmrClust : Kelley et al. (1996)

MolProbity : 4.02b-467Mogul : 1.8.5 (274361), CSD as541be (2020)

Percentile statistics : 20191225.v01 (using entries in the PDB archive December 25th 2019)RCI : v_1n_11_5_13_A (Berjanski et al., 2005)

PANAV : Wang et al. (2010)ShiftChecker : 2.11

Ideal geometry (proteins) : Engh & Huber (2001)Ideal geometry (DNA, RNA) : Parkinson et al. (1996)

Validation Pipeline (wwPDB-VP) : 2.11

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp



https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#references

Full wwPDB NMR Structure Validation Report 2MGT

1 Overall quality at a glance iO

The following experimental techniques were used to determine the structure:SOLUTION NMR

The overall completeness of chemical shifts assignment is 40%.

Percentile scores (ranging between 0-100) for global validation metrics of the entry are shown inthe following graphic. The table shows the number of entries on which the scores are based.

MetricWhole archive(#Entries)

NMR archive(#Entries)

Clashscore 158937 12864Ramachandran outliers 154571 11451

Sidechain outliers 154315 11428

The table below summarises the geometric issues observed across the polymeric chains and their�t to the experimental data. The red, orange, yellow and green segments indicate the fractionof residues that contain outliers for >=3, 2, 1 and 0 types of geometric quality criteria. A cyansegment indicates the fraction of residues that are not part of the well-de�ned cores, and a grey seg-ment represents the fraction of residues that are not modelled. The numeric value for each fractionis indicated below the corresponding segment, with a dot representing fractions <=5%

Mol Chain Length Quality of chain

1 A 18

1 B 18

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#overall_quality


2 Ensemble composition and analysis iO

This entry contains 20 models. Model 1 is the overall representative, medoid model (most similarto other models).

The following residues are included in the computation of the global validation metrics.

Well-de�ned (core) protein residuesWell-de�ned core Residue range (total) Backbone RMSD (Å) Medoid model

1 A:1-A:16, B:1-B:16 (32) 1.21 1

Ill-de�ned regions of proteins are excluded from the global statistics.

Ligands and non-protein polymers are included in the analysis.

The models can be grouped into 4 clusters and 2 single-model clusters were found.

Cluster number Models1 1, 7, 8, 10, 13, 16, 202 3, 4, 11, 15, 183 2, 9, 12, 194 6, 17

Single-model clusters 5; 14

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#ensemble_composition


3 Entry composition iO

There are 2 unique types of molecules in this entry. The entry contains 539 atoms, of which 252are hydrogens and 0 are deuteriums.

� Molecule 1 is a protein called Amyloid beta A4 protein.

Mol Chain Residues Atoms Trace

1 A 18Total C H N O269 86 126 29 28

1

1 B 18Total C H N O269 86 126 29 28

1

There are 6 discrepancies between the modelled and reference sequences:

Chain Residue Modelled Actual Comment ReferenceA 0 ACE - acetylation UNP P05067A 6 ARG HIS engineered mutation UNP P05067A 17 NH2 - amidation UNP P05067B 0 ACE - acetylation UNP P05067B 6 ARG HIS engineered mutation UNP P05067B 17 NH2 - amidation UNP P05067

� Molecule 2 is ZINC ION (three-letter code: ZN) (formula: Zn).

Mol Chain Residues Atoms

2 A 1Total Zn1 1

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#entry_composition


4 Residue-property plots iO

4.1 Average score per residue in the NMR ensemble

These plots are provided for all protein, RNA and DNA chains in the entry. The �rst graphic is thesame as shown in the summary in section 1 of this report. The second graphic shows the sequencewhere residues are colour-coded according to the number of geometric quality criteria for whichthey contain at least one outlier: green = 0, yellow = 1, orange = 2 and red = 3 or more. Stretchesof 2 or more consecutive residues without any outliers are shown as green connectors. Residueswhich are classi�ed as ill-de�ned in the NMR ensemble, are shown in cyan with an underlinecolour-coded according to the previous scheme. Residues which were present in the experimentalsample, but not modelled in the �nal structure are shown in grey.

• Molecule 1: Amyloid beta A4 protein

Chain A:

?0

Y10

?17


Chain B:

?0

Y10

?17

4.2 Scores per residue for each member of the ensemble

Colouring as in section 4.1 above.

4.2.1 Score per residue for model 1 (medoid)


Chain A:

?0

Y10

E11

?17


Chain B:

?0

Y10

E11

?17

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#residue_plots


4.2.2 Score per residue for model 2


Chain A:

?0

Y10

?17


Chain B:

?0

Y10

?17



Chain A:

?0

R5

Y10

K16

?17


Chain B:

?0

E3

R6

Y10

?17



Chain A:

?0

R5

Y10

?17


Chain B:

?0

Y10

?17




Chain A:

?0

R6

Y10

?17


Chain B:

?0

R6

Y10

H14

?17



Chain A:

?0

R6

Y10

?17


Chain B:

?0

Y10

?17



Chain A:

?0

S8

G9

Y10

?17


Chain B:

?0

Y10

?17




Chain A:

?0

Y10

?17


Chain B:

?0

D7

Y10

?17



Chain A:

?0

D1

Y10

?17


Chain B:

?0

Y10

H14

?17



Chain A:

?0

R5

Y10

?17


Chain B:

?0

Y10

?17




Chain A:

?0

R6

Y10

?17


Chain B:

?0

Y10

?17



Chain A:

?0

R5

Y10

?17


Chain B:

?0

E3

F4

R5

R6

Y10

E11

?17



Chain A:

?0

D1

A2

Y10

?17


Chain B:

?0

Y10

Q15

K16

?17




Chain A:

?0

D1

Y10

?17


Chain B:

?0

R6

Y10

?17



Chain A:

?0

Y10

?17


Chain B:

?0

R5

Y10

E11

?17



Chain A:

?0

R5

Y10

?17


Chain B:

?0

Y10

?17




Chain A:

?0

Y10

H14

?17


Chain B:

?0

Y10

H14

Q15

K16

?17



Chain A:

?0

E3

Y10

?17


Chain B:

?0

R5

Y10

?17



Chain A:

?0

D1

R5

Y10

?17


Chain B:

?0

Y10

?17




Chain A:

?0

R6

Y10

Q15

K16

?17


Chain B:

?0

D1

Y10

?17


5 Re�nement protocol and experimental data overview iO

The models were re�ned using the following method: simulated annealing.

Of the 100 calculated structures, 20 were deposited, based on the following criterion: structures

with the lowest energy.

The following table shows the software used for structure solution, optimisation and re�nement.

Software name Classi�cation VersionGROMACS re�nement 4.5.4CPMD geometry optimization

The following table shows chemical shift validation statistics as aggregates over all chemical shift�les. Detailed validation can be found in section 6 of this report.

Chemical shift �le(s) input_cs.cifNumber of chemical shift lists 3Total number of shifts 528Number of shifts mapped to atoms 528Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0Assignment completeness (well-de�ned parts) 40%

No validations of the models with respect to experimental NMR restraints is performed at thistime.

COVALENT-GEOMETRY INFOmissingINFO

5.1 Too-close contacts iO

In the following table, the Non-H and H(model) columns list the number of non-hydrogen atomsand hydrogen atoms in each chain respectively. The H(added) column lists the number of hydrogenatoms added and optimized by MolProbity. The Clashes column lists the number of clashesaveraged over the ensemble.

Mol Chain Non-H H(model) H(added) Clashes1 A 139 121 121 0±01 B 139 121 121 0±0All All 5580 4840 4840 1

The all-atom clashscore is de�ned as the number of clashes found per 1000 atoms (includinghydrogen atoms). The all-atom clashscore for this structure is 0.

All unique clashes are listed below, sorted by their clash magnitude.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#refinement_protocol

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#close_contacts


Atom-1 Atom-2 Clash(Å) Distance(Å)Models

Worst Total

1:A:14:HIS:CE1 1:B:15:GLN:HE21 0.45 2.30 17 1

5.2 Torsion angles iO

5.2.1 Protein backbone iO

In the following table, the Percentiles column shows the percent Ramachandran outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the backbone conformationwas analysed and the total number of residues.

Mol Chain Analysed Favoured Allowed Outliers Percentiles

1 A 16/18 (89%) 13±1 (84±6%) 2±1 (15±6%) 0±0 (1±3%) 16 63

1 B 16/18 (89%) 12±1 (76±8%) 4±1 (23±8%) 0±0 (1±2%) 21 69

All All 640/720 (89%) 512 (80%) 121 (19%) 7 (1%) 18 66

All 4 unique Ramachandran outliers are listed below. They are sorted by the frequency of occur-rence in the ensemble.

Mol Chain Res Type Models (Total)1 A 5 ARG 31 B 14 HIS 21 B 6 ARG 11 A 8 SER 1

5.2.2 Protein sidechains iO

In the following table, the Percentiles column shows the percent sidechain outliers of the chainas a percentile score with respect to all PDB entries followed by that with respect to all NMRentries. The Analysed column shows the number of residues for which the sidechain conformationwas analysed and the total number of residues.

Mol Chain Analysed Rotameric Outliers Percentiles

1 A 14/14 (100%) 13±0 (90±3%) 1±0 (10±3%) 12 58

1 B 14/14 (100%) 13±1 (90±4%) 1±1 (10±4%) 12 58

All All 560/560 (100%) 506 (90%) 54 (10%) 12 58

All 12 unique residues with a non-rotameric sidechain are listed below. They are sorted by thefrequency of occurrence in the ensemble.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#torsion_angles

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#protein_backbone

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#protein_sidechains


Mol Chain Res Type Models (Total)1 A 10 TYR 201 B 10 TYR 201 A 1 ASP 31 B 5 ARG 21 A 5 ARG 21 B 7 ASP 11 A 16 LYS 11 A 15 GLN 11 B 11 GLU 11 B 15 GLN 11 B 1 ASP 11 B 14 HIS 1

5.2.3 RNA iO

There are no RNA molecules in this entry.

5.3 Non-standard residues in protein, DNA, RNA chains iO

There are no non-standard protein/DNA/RNA residues in this entry.

5.4 Carbohydrates iO

There are no carbohydrates in this entry.

5.5 Ligand geometry iO

Of 1 ligands modelled in this entry, 1 is monoatomic - leaving 0 for Mogul analysis.

5.6 Other polymers iO

There are no such molecules in this entry.

5.7 Polymer linkage issues iO

There are no chain breaks in this entry.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#rna

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#nonstandard_residues_and_ligands




https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#polymer_linkage


6 Chemical shift validation iO

The completeness of assignment taking into account all chemical shift lists is 40% for the well-de�ned parts and 40% for the entire structure.

6.1 Chemical shift list 1

File name: input_cs.cif

Chemical shift list name: Assigned_chemical_shifts_2

6.1.1 Bookkeeping iO

The following table shows the results of parsing the chemical shift list and reports the number ofnuclei with statistically unusual chemical shifts.

Total number of shifts 172Number of shifts mapped to atoms 172Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0

Number of shift outliers (ShiftChecker) 0

6.1.2 Chemical shift referencing iO

No chemical shift referencing corrections were calculated (not enough data).

6.1.3 Completeness of resonance assignments iO

The following table shows the completeness of the chemical shift assignments for the well-de�nedregions of the structure. The overall completeness is 37%, i.e. 159 atoms were assigned a chemicalshift out of a possible 430. 0 out of 2 assigned methyl groups (LEU and VAL) were assignedstereospeci�cally.

Total 1H 13C 15NBackbone 59/160 (37%) 32/64 (50%) 16/64 (25%) 11/32 (34%)Sidechain 78/208 (38%) 54/124 (44%) 24/68 (35%) 0/16 (0%)Aromatic 22/62 (35%) 14/34 (41%) 8/24 (33%) 0/4 (0%)Overall 159/430 (37%) 100/222 (45%) 48/156 (31%) 11/52 (21%)

The following table shows the completeness of the chemical shift assignments for the full structure.The overall completeness is 37%, i.e. 159 atoms were assigned a chemical shift out of a possible430. 0 out of 2 assigned methyl groups (LEU and VAL) were assigned stereospeci�cally.

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#chemical_shifts

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#cs_bookkeeping

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#cs_referencing

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#cs_completeness



6.1.4 Statistically unusual chemical shifts iO

There are no statistically unusual chemical shifts.

6.1.5 Random Coil Index (RCI) plots iO

The image below reports random coil index values for the protein chains in the structure. Theheight of each bar gives a probability of a given residue to be disordered, as predicted fromthe available chemical shifts and the amino acid sequence. A value above 0.2 is an indicationof signi�cant predicted disorder. The colour of the bar shows whether the residue is in the well-de�ned core (black) or in the ill-de�ned residue ranges (cyan), as described in section 2 on ensemblecomposition.

Random coil index (RCI) for chain B:



Chemical shift list name: Assigned_chemical_shifts_3



Total number of shifts 174Number of shifts mapped to atoms 174

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#cs_outliers

https://www.wwpdb.org/validation/2017/NMRValidationReportHelp#cs_rci



Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0












The image below reports random coil index values for the protein chains in the structure. Theheight of each bar gives a probability of a given residue to be disordered, as predicted fromthe available chemical shifts and the amino acid sequence. A value above 0.2 is an indication






of signi�cant predicted disorder. The colour of the bar shows whether the residue is in the well-de�ned core (black) or in the ill-de�ned residue ranges (cyan), as described in section 2 on ensemblecomposition.




Chemical shift list name: assigned_chem_shift_list_1



Total number of shifts 182Number of shifts mapped to atoms 182Number of unparsed shifts 0Number of shifts with mapping errors 0Number of shifts with mapping warnings 0
















The image below reports random coil index values for the protein chains in the structure. Theheight of each bar gives a probability of a given residue to be disordered, as predicted fromthe available chemical shifts and the amino acid sequence. A value above 0.2 is an indicationof signi�cant predicted disorder. The colour of the bar shows whether the residue is in the well-de�ned core (black) or in the ill-de�ned residue ranges (cyan), as described in section 2 on ensemblecomposition.




full wwpdb nmr structure validation report o i - rcsb

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