X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherstructure of as-isolated hydrogenase-1 refined at 1.67A resolution

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.8298PEG4000, LiSO4, ferricyanide, OH-NQ, pH 5.8, VAPOR DIFFUSION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.17α = 90
b = 98.16β = 90
c = 183.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDfocusing mirrors2011-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

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
1210085.10.11112.062.893189394101239-317.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.184.60.3693.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTstructure of as-isolated hydrogenase-1 refined at 1.67A resolution225101213101213507687.610.14240.14240.14060.1769RANDOM11.328
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]
0.170.72-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.962
r_dihedral_angle_4_deg15.8
r_dihedral_angle_3_deg12.771
r_dihedral_angle_1_deg5.749
r_scangle_it4.091
r_scbond_it2.7
r_mcangle_it1.695
r_angle_refined_deg1.259
r_mcbond_it1.067
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.962
r_dihedral_angle_4_deg15.8
r_dihedral_angle_3_deg12.771
r_dihedral_angle_1_deg5.749
r_scangle_it4.091
r_scbond_it2.7
r_mcangle_it1.695
r_angle_refined_deg1.259
r_mcbond_it1.067
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13182
Nucleic Acid Atoms
Solvent Atoms1232
Heterogen Atoms116

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MxCuBEdata collection
XDSdata reduction
REFMACphasing