- PDB-4d4x: Nitrosyl complex of the D121I variant of cytochrome c prime from ... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4d4x
Title
Nitrosyl complex of the D121I variant of cytochrome c prime from Alcaligenes xylosoxidans
Components
CYTOCHROME C'
Keywords
ELECTRON TRANSPORT / PROXIMAL NO / GAS SENSING / NITRIC OXIDE
Function / homology
Function and homology information
electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding Similarity search - Function
Cytochrome c prime, subgroup / Cytochrome c prime / Cytochrome c class II profile. / Cytochrome c, class II / Cytochrome C' / Cytochrome c/b562 / Cytochrome c/b562 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha Similarity search - Domain/homology
Monochromator: SI MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.3→13.4 Å / Num. obs: 37815 / % possible obs: 98.7 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shell
Resolution: 1.3→1.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.73 / % possible all: 98.6
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
XDS
datareduction
Aimless
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.3→46.03 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.07 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.052 / 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
0.21444
1883
5 %
RANDOM
Rwork
0.16873
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obs
0.17095
35829
98.55 %
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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