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High-resolution structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant
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 6.1 298 VAPOR DIFFUSION, ANAEROBIC, 298 K, PEG 6000, MES, HEPES, PH 6.1
Crystal Properties Matthews coefficient Solvent content 2.03 39.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.69 α = 90 b = 100.85 β = 105.96 c = 116.7 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 2009-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.15 46 95.9 0.079 7.95 3.61 487248 -3 12
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 1.15 1.22 88 0.68 1.22 3.16
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 1.22 30 393990 20888 97.38 0.12202 0.12043 0.1317 0.152 0.161 RANDOM 10.508
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] 0.44 0.05 -0.29 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_sphericity_free 25.813 r_dihedral_angle_4_deg 15.382 r_rigid_bond_restr 13.42 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 6.122 r_sphericity_bonded 6.118 r_angle_other_deg 3.579 r_scbond_it 1.749 r_angle_refined_deg 1.662
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.402 r_sphericity_free 25.813 r_dihedral_angle_4_deg 15.382 r_rigid_bond_restr 13.42 r_dihedral_angle_3_deg 12.237 r_dihedral_angle_1_deg 6.122 r_sphericity_bonded 6.118 r_angle_other_deg 3.579 r_scbond_it 1.749 r_angle_refined_deg 1.662 r_mcangle_it 1.397 r_mcbond_it 1.148 r_mcbond_other 1.146 r_chiral_restr 0.107 r_gen_planes_other 0.018 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 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_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 12287 Nucleic Acid Atoms Solvent Atoms 1752 Heterogen Atoms 156
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing