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Structure of the V74C large subunit mutant of D. fructosovorans NiFe- hydrogenase
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 6.3 INSIDE ANAEROBIC GLOVE BOX, PEG6000, MES, PH 7.3
Crystal Properties Matthews coefficient Solvent content 2.1 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.72 α = 90.21 b = 99.8 β = 98.61 c = 190.8 γ = 90.11
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 2009-11-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.7 30 85 0.05 10.3 1.9 414223
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) 1 1.7 1.8 75.3 0.36 2.4 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 1.7 20 393108 20971 84.96 0.13905 0.13659 0.1373 0.18539 0.1862 RANDOM 21.001
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] -0.46 -1.07 -0.12 0.04 0.1 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_sphericity_free 22.467 r_dihedral_angle_4_deg 16.398 r_sphericity_bonded 15.09 r_dihedral_angle_3_deg 13.622 r_dihedral_angle_1_deg 5.932 r_rigid_bond_restr 2.705 r_scbond_it 2.242 r_mcangle_it 1.841 r_mcbond_it 1.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.05 r_sphericity_free 22.467 r_dihedral_angle_4_deg 16.398 r_sphericity_bonded 15.09 r_dihedral_angle_3_deg 13.622 r_dihedral_angle_1_deg 5.932 r_rigid_bond_restr 2.705 r_scbond_it 2.242 r_mcangle_it 1.841 r_mcbond_it 1.601 r_angle_refined_deg 1.421 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 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_other r_mcangle_other 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 Atoms Number Protein Atoms 36866 Nucleic Acid Atoms Solvent Atoms 3410 Heterogen Atoms 272
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing