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[FeFe]-hydrogenase Oxygen Inactivation is Initiated by the Modification and Degradation of the H cluster 2Fe Subcluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LX4 PDB entry 3lx4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.5 298 25.5% Polyethylene Glycol 8,000, 0.085 M Sodium Cacodylate, 0.17 M Sodium Acetate Trihydrate, 1mM Sodium Dithionite, pH 6.5, SMALL TUBES, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.645 α = 90 b = 70.964 β = 91.91 c = 94.686 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 77 PIXEL DECTRIS PILATUS 6M 2013-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 1.73450 SSRL BL12-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.29 94.633 88.2 46625 41114 2 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.41 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 3lx4 2.29 35 3 46625 39011 2097 88.17 0.20882 0.2065 0.2168 0.25211 0.2552 RANDOM 49.48
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] 1.78 -0.01 -1.65 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.337 r_dihedral_angle_4_deg 18.233 r_dihedral_angle_3_deg 17.247 r_long_range_B_refined 8.401 r_long_range_B_other 8.343 r_dihedral_angle_1_deg 7.298 r_scangle_other 5.547 r_mcangle_it 4.491 r_mcangle_other 4.491 r_scbond_other 3.924
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.337 r_dihedral_angle_4_deg 18.233 r_dihedral_angle_3_deg 17.247 r_long_range_B_refined 8.401 r_long_range_B_other 8.343 r_dihedral_angle_1_deg 7.298 r_scangle_other 5.547 r_mcangle_it 4.491 r_mcangle_other 4.491 r_scbond_other 3.924 r_scbond_it 3.923 r_mcbond_other 3.024 r_mcbond_it 3.023 r_angle_refined_deg 2.093 r_angle_other_deg 1.029 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6282 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 22
Software Software Software Name Purpose Blu-Ice data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling