3WB0

HcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3BRC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529820 %(w/v) PEG 8000, 0.1 M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1141.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.96α = 90
b = 119.34β = 115.14
c = 55.65γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-06-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.000SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.95094.90.08511.1746660-330.577
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9287.70.3230.4122.88

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3BRC1.9147.9445988232994.260.22910.22660.2752RANDOM29.9177
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
-0.080.070.1-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_3_deg18.138
r_dihedral_angle_4_deg17.058
r_dihedral_angle_1_deg6.166
r_scbond_it3.177
r_mcangle_it2.652
r_angle_refined_deg2.031
r_mcbond_it1.87
r_chiral_restr0.131
r_bond_refined_d0.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.394
r_dihedral_angle_3_deg18.138
r_dihedral_angle_4_deg17.058
r_dihedral_angle_1_deg6.166
r_scbond_it3.177
r_mcangle_it2.652
r_angle_refined_deg2.031
r_mcbond_it1.87
r_chiral_restr0.131
r_bond_refined_d0.017
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4956
Nucleic Acid Atoms
Solvent Atoms376
Heterogen Atoms148

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling