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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, 22% (W/V) PEG 3350, 200 MM LISO4, 150 MM NACL, 1 MM TCEP, 0.02 % (W/V) DDM
Crystal Properties Matthews coefficient Solvent content 2.2 44.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.757 α = 90 b = 97.77 β = 90 c = 183.288 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 2015-03-05 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 1.25 45.8 99.9 0.13 11.6 12 460946 -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 1.25 1.27 99.9 1.5 1.4 11.7
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 1.25 91.64 437800 22969 99.84 0.12894 0.12752 0.1426 0.15664 0.1676 RANDOM 13.706
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] 0.23 0.25 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_sphericity_free 17.431 r_dihedral_angle_4_deg 16.713 r_dihedral_angle_3_deg 12.092 r_dihedral_angle_1_deg 6.133 r_sphericity_bonded 5.534 r_rigid_bond_restr 3.568 r_angle_refined_deg 1.938 r_scangle_it 1.833 r_scbond_it 1.779
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_sphericity_free 17.431 r_dihedral_angle_4_deg 16.713 r_dihedral_angle_3_deg 12.092 r_dihedral_angle_1_deg 6.133 r_sphericity_bonded 5.534 r_rigid_bond_restr 3.568 r_angle_refined_deg 1.938 r_scangle_it 1.833 r_scbond_it 1.779 r_mcangle_it 1.327 r_mcbond_it 1.13 r_mcbond_other 1.13 r_angle_other_deg 1.127 r_symmetry_vdw_refined 0.267 r_nbd_refined 0.244 r_nbd_other 0.225 r_symmetry_vdw_other 0.203 r_nbtor_refined 0.182 r_metal_ion_refined 0.139 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.12 r_chiral_restr 0.117 r_nbtor_other 0.095 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_xyhbond_nbd_other 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 13164 Nucleic Acid Atoms Solvent Atoms 973 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing