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Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WUI PDB ENTRY 1WUI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 277 Imidazole, sodium citrate, pH 8.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.67 66.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 205.75 α = 90 b = 216.96 β = 90 c = 119.8 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD mirrors 2009-02-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.1 48.06 95 0.057 18.5 4.16 295408 295408
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.1 2.19 90.2 0.296 4.9 4.22
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1WUI 2.1 30 294160 294160 15482 100 0.13952 0.138 0.1506 0.16811 0.1778 RANDOM 29.902
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] 1.09 -1.63 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.683 r_dihedral_angle_4_deg 18.008 r_dihedral_angle_3_deg 16.55 r_dihedral_angle_1_deg 6.916 r_scangle_it 6.524 r_scbond_it 4.293 r_mcangle_it 2.262 r_angle_refined_deg 1.936 r_mcbond_it 1.355 r_chiral_restr 0.339
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.683 r_dihedral_angle_4_deg 18.008 r_dihedral_angle_3_deg 16.55 r_dihedral_angle_1_deg 6.916 r_scangle_it 6.524 r_scbond_it 4.293 r_mcangle_it 2.262 r_angle_refined_deg 1.936 r_mcbond_it 1.355 r_chiral_restr 0.339 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25641 Nucleic Acid Atoms Solvent Atoms 1925 Heterogen Atoms 146
Software Software Software Name Purpose REFMAC refinement CNS refinement XDS data scaling XDS data reduction XSCALE data scaling CNS phasing