5Y34

Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibrio marinus in a ferricyanide-oxidized condition


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1M PIPES, 15% PEG 3350, 300MM LITHIUM SULFATE, 5MM DTT, PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5651.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.628α = 90
b = 116.943β = 91.42
c = 113.337γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray90CCDRAYONIX MX-2252010-10-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9000SPring-8BL44XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.322099.212.63.8459508
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)
11.321.3497.30.4963.23.2

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 REPLACEMENTTHROUGHOUT3AYX1.3219.894255562244297.340.131990.130630.15804RANDOM19.001
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]
2.660.84-0.74-1.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_sphericity_free32.164
r_dihedral_angle_4_deg15.503
r_sphericity_bonded15.012
r_dihedral_angle_3_deg11.9
r_dihedral_angle_1_deg5.934
r_rigid_bond_restr2.509
r_angle_refined_deg1.347
r_chiral_restr0.09
r_bond_refined_d0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.129
r_sphericity_free32.164
r_dihedral_angle_4_deg15.503
r_sphericity_bonded15.012
r_dihedral_angle_3_deg11.9
r_dihedral_angle_1_deg5.934
r_rigid_bond_restr2.509
r_angle_refined_deg1.347
r_chiral_restr0.09
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13529
Nucleic Acid Atoms
Solvent Atoms2189
Heterogen Atoms88

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing