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The Mechanism of Hydrogen Activation by NiFe-hydrogenases
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3USC PDB ENTRY 3USC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 100 MM BIS-TRIS PH 6.0, 21 % PEG 3350, 200 MM LISO4, 150 MM NACL
Crystal Properties Matthews coefficient Solvent content 2.14 42.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.855 α = 90 b = 98.979 β = 90 c = 185.207 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M MIRRORS 2015-07-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 Diamond I04-1
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 1.1 49.5 95.5 0.16 10.5 12.8 665775 -3
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 1.1 1.12 92.1 1.5 1.7 12.3
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 3USC 1.1 92.78 632387 33298 95.27 0.12693 0.12612 0.1389 0.14238 0.1533 RANDOM 10.686
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] 0.2 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.317 r_sphericity_free 18.264 r_dihedral_angle_4_deg 16.302 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_1_deg 6.112 r_sphericity_bonded 5.275 r_rigid_bond_restr 3.035 r_angle_refined_deg 1.866 r_scangle_it 1.662 r_scbond_it 1.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.317 r_sphericity_free 18.264 r_dihedral_angle_4_deg 16.302 r_dihedral_angle_3_deg 11.911 r_dihedral_angle_1_deg 6.112 r_sphericity_bonded 5.275 r_rigid_bond_restr 3.035 r_angle_refined_deg 1.866 r_scangle_it 1.662 r_scbond_it 1.403 r_angle_other_deg 1.073 r_mcangle_it 1.054 r_mcbond_it 0.829 r_mcbond_other 0.829 r_symmetry_vdw_refined 0.244 r_xyhbond_nbd_other 0.243 r_metal_ion_refined 0.238 r_nbd_refined 0.229 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.161 r_nbd_other 0.152 r_symmetry_vdw_other 0.139 r_chiral_restr 0.107 r_symmetry_hbond_refined 0.087 r_nbtor_other 0.07 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other 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 13163 Nucleic Acid Atoms Solvent Atoms 1093 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing