8POV

Crystal Structure of the C19G/C120G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the H2-reduced state at 1.92 A Resolution.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.527720% - 30% PEG3350, 0.1M BIS-TRIS PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.0238.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.201α = 90
b = 95.506β = 90
c = 118.978γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252012-01-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.9234.21000.0919.94.964415
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.922.021000.5310.862.15

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9234.260918324599.690.168260.166560.19938RANDOM29.668
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]
-0.24-1.51.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.4
r_sphericity_free33.096
r_dihedral_angle_4_deg16.956
r_dihedral_angle_3_deg12.598
r_sphericity_bonded6.676
r_dihedral_angle_1_deg5.52
r_long_range_B_refined3.458
r_long_range_B_other3.458
r_mcangle_it2.063
r_mcangle_other2.063
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.4
r_sphericity_free33.096
r_dihedral_angle_4_deg16.956
r_dihedral_angle_3_deg12.598
r_sphericity_bonded6.676
r_dihedral_angle_1_deg5.52
r_long_range_B_refined3.458
r_long_range_B_other3.458
r_mcangle_it2.063
r_mcangle_other2.063
r_scangle_other1.766
r_rigid_bond_restr1.616
r_mcbond_it1.581
r_mcbond_other1.581
r_scbond_it1.47
r_scbond_other1.47
r_angle_refined_deg1.076
r_angle_other_deg0.768
r_chiral_restr0.061
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6780
Nucleic Acid Atoms
Solvent Atoms530
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing