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The Mechanism of Hydrogen Activation by NiFe-hydrogenases and the Importance of the active site Arginine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3USC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 100 mM Bis tris pH 5.5-5.9,
150 mM NaCl
200 mM Li2SO4
19-21% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.06 40.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.521 α = 90 b = 97.405 β = 90 c = 183.229 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 6M MIRRORS 2014-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 1.4 48.75 97 0.13 13.1 13.1 317004 -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 1.4 1.42 75.3 1.35 1.7 10.1
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3usc 1.4 48.75 316924 15658 96.835 0.141 0.1397 0.1397 0.1602 0.1602 12.322
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] 0.141 -0.046 -0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.294 r_dihedral_angle_4_deg 16.799 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 6.558 r_lrange_it 4.012 r_lrange_other 3.918 r_scangle_it 3.187 r_scangle_other 3.187 r_scbond_other 2.147 r_scbond_it 2.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.294 r_dihedral_angle_4_deg 16.799 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 6.558 r_lrange_it 4.012 r_lrange_other 3.918 r_scangle_it 3.187 r_scangle_other 3.187 r_scbond_other 2.147 r_scbond_it 2.146 r_angle_refined_deg 2.091 r_angle_other_deg 1.633 r_mcangle_it 1.464 r_mcangle_other 1.464 r_mcbond_other 1.033 r_mcbond_it 1.032 r_nbd_refined 0.234 r_symmetry_nbd_refined 0.234 r_symmetry_xyhbond_nbd_refined 0.229 r_nbd_other 0.214 r_symmetry_nbd_other 0.185 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.157 r_metal_ion_refined 0.112 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.087 r_symmetry_xyhbond_nbd_other 0.075 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13166 Nucleic Acid Atoms Solvent Atoms 1340 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing