- PDB-5ak8: Structure of C351A mutant of Porphyromonas gingivalis peptidylarg... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5ak8
Title
Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase
Components
PEPTIDYLARGININE DEIMINASE
Keywords
HYDROLASE / PPAD
Function / homology
Function and homology information
Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amidines / agmatine deiminase activity / putrescine biosynthetic process / protein-arginine deiminase activity / extracellular region Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.97625 Å / Relative weight: 1
Reflection
Resolution: 1.48→64.8 Å / Num. obs: 73831 / % possible obs: 95.3 % / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.4
Reflection shell
Resolution: 1.48→1.52 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.1 / % possible all: 93.9
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0107
refinement
PHASER
phasing
Refinement
Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→64.8 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 3.064 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.16444
3636
4.9 %
RANDOM
Rwork
0.12737
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obs
0.12921
70193
95.13 %
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Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK