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Structure of the V74M large subunit mutant of NI-FE hydrogenase in an oxidized state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YQW PDB ENTRY 1YQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 PEG6000, GLYCEROL, pH6.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.4 α = 90 b = 99.2 β = 92.8 c = 182.3 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r mirrors 2008-04-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97623 ESRF ID29
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.7 20 98.7 0.051 0.051 15.18 3.42 61024 60250 42.6
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) Redundancy Number Unique Reflections (All) 1 2.7 2.8 98.1 0.288 0.288 4.31 3.07 6288
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 1YQW 2.7 20 60250 57315 2935 98.73 0.206 0.203 0.2051 0.247 0.2471 RANDOM 41.52
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] 2.17 2.44 -0.96 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_4_deg 15.862 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_1_deg 6.013 r_scangle_it 1.541 r_angle_refined_deg 1.451 r_scbond_it 1.054 r_mcangle_it 0.563 r_mcbond_it 0.367 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.532 r_dihedral_angle_4_deg 15.862 r_dihedral_angle_3_deg 15.823 r_dihedral_angle_1_deg 6.013 r_scangle_it 1.541 r_angle_refined_deg 1.451 r_scbond_it 1.054 r_mcangle_it 0.563 r_mcbond_it 0.367 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.286 r_symmetry_vdw_refined 0.242 r_metal_ion_refined 0.211 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.097 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 18400 Nucleic Acid Atoms Solvent Atoms 562 Heterogen Atoms 138
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling