3H3X

Structure of the V74M large subunit mutant of NI-FE hydrogenase in an oxidized state


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6293PEG6000, GLYCEROL, pH6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1141.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.4α = 90
b = 99.2β = 92.8
c = 182.3γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2008-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.97623ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.72098.70.0510.05115.183.42610246025042.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.898.10.2880.2884.313.076288

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1YQW2.7206025057315293598.730.2060.2030.247RANDOM41.52
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]
2.172.44-0.96-0.98
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg15.862
r_dihedral_angle_3_deg15.823
r_dihedral_angle_1_deg6.013
r_scangle_it1.541
r_angle_refined_deg1.451
r_scbond_it1.054
r_mcangle_it0.563
r_mcbond_it0.367
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.532
r_dihedral_angle_4_deg15.862
r_dihedral_angle_3_deg15.823
r_dihedral_angle_1_deg6.013
r_scangle_it1.541
r_angle_refined_deg1.451
r_scbond_it1.054
r_mcangle_it0.563
r_mcbond_it0.367
r_nbtor_refined0.309
r_symmetry_hbond_refined0.286
r_symmetry_vdw_refined0.242
r_metal_ion_refined0.211
r_nbd_refined0.21
r_xyhbond_nbd_refined0.175
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms18400
Nucleic Acid Atoms
Solvent Atoms562
Heterogen Atoms138

Software

Software
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling