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Structure of the unready Ni-A state of the S499C 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 VAPOR DIFFUSION 6.2 298 VAPOR DIFFUSION, UNDER AIR, 298 K, PEG 6000, MES, TRIS/HCL, PH 6.2
Crystal Properties Matthews coefficient Solvent content 2.22 44.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.43 α = 90 b = 98.96 β = 91.19 c = 184.95 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 CCD 2001-09-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 ESRF ID14-1
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 1.8 29.83 96.2 0.119 6.14 4.21 209473 -3 22.8
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 1.8 1.92 82.2 0.479 1.74 3.11
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 1.8 29.83 198944 10529 96.13 0.15284 0.1509 0.153 0.18977 0.1914 RANDOM 19.994
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] 1.47 -0.16 -0.47 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 16.398 r_dihedral_angle_3_deg 13.039 r_dihedral_angle_1_deg 5.96 r_scbond_it 2.018 r_mcangle_it 1.751 r_angle_refined_deg 1.453 r_mcbond_it 1.204 r_chiral_restr 0.098 r_bond_refined_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.009 r_dihedral_angle_4_deg 16.398 r_dihedral_angle_3_deg 13.039 r_dihedral_angle_1_deg 5.96 r_scbond_it 2.018 r_mcangle_it 1.751 r_angle_refined_deg 1.453 r_mcbond_it 1.204 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18424 Nucleic Acid Atoms Solvent Atoms 2034 Heterogen Atoms 149
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing