X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5298PEG4000, LiSO4, DTT, DMM, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.71α = 90
b = 97.4β = 90
c = 183.73γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rToroidal mirror2011-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-11.00407ESRFID23-1

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
11.4729.57990.06910.352.647547509283897-316.861
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)
11.471.598.90.3732.79

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 1.67 Angstroem resolution1.47252838732838731410499.840.12430.12430.12240.16RANDOM12.7922
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]
-0.230.33-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_4_deg15.264
r_dihedral_angle_3_deg11.887
r_scangle_it5.671
r_dihedral_angle_1_deg5.619
r_scbond_it4.162
r_mcangle_it2.87
r_rigid_bond_restr2.204
r_mcbond_it2.029
r_angle_refined_deg1.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.24
r_dihedral_angle_4_deg15.264
r_dihedral_angle_3_deg11.887
r_scangle_it5.671
r_dihedral_angle_1_deg5.619
r_scbond_it4.162
r_mcangle_it2.87
r_rigid_bond_restr2.204
r_mcbond_it2.029
r_angle_refined_deg1.223
r_chiral_restr0.085
r_bond_refined_d0.01
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13182
Nucleic Acid Atoms
Solvent Atoms1606
Heterogen Atoms132

Software

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