- PDB-4d4n: Nitrosyl complex of the D121A 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: 4d4n
Title
Nitrosyl complex of the D121A variant of cytochrome c prime from Alcaligenes xylosoxidans
Components
CYTOCHROME C'
Keywords
OXIDOREDUCTASE / PROXIMAL NO / GAS SENSING
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: 1.45→9.3 Å / Num. obs: 27816 / % possible obs: 97.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shell
Resolution: 1.45→1.5 Å / Redundancy: 6 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.5 / % possible all: 97.1
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0073
refinement
HKL-2000
datareduction
HKL-2000
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.45→46.55 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.872 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.062 / 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
0.20074
1399
5 %
RANDOM
Rwork
0.15919
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obs
0.1613
26396
97.67 %
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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