- PDB-4cjo: Spectroscopically-validated structure of ferrous cytochrome c pri... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 4cjo
Title
Spectroscopically-validated structure of ferrous cytochrome c prime from Alcaligenes xylosoxidans, reduced at 180K using X-rays
Components
CYTOCHROME C'
Keywords
ELECTRON TRANSPORT / RESONANCE RAMAN / VALIDATION / GAS SENSOR / LIGAND DISCRIMINATION / FERRIC / HAEM / HEME / RADIOLYSIS
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 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 1 Å / Relative weight: 1
Reflection
Resolution: 1.55→46.5 Å / Num. obs: 21722 / % possible obs: 93.9 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shell
Resolution: 1.55→1.58 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.4 / % possible all: 96
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Processing
Software
Name
Version
Classification
REFMAC
5.8.0049
refinement
XDS
datareduction
SCALA
datascaling
Refinement
Method to determine structure: OTHER Starting model: NONE Resolution: 1.55→46.48 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.793 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / 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
0.25119
1156
5.3 %
RANDOM
Rwork
0.2312
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obs
0.23222
20562
92.26 %
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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