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Crystal Structure of E. coli hydrogenase-1 in a ferricyanide-oxidized form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other structure of as-isolated hydrogenase-1 refined at 1.67A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.8 298 PEG4000, LiSO4, ferricyanide, OH-NQ, pH 5.8, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.09 41.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.17 α = 90 b = 98.16 β = 90 c = 183.96 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 CCD MARMOSAIC 225 mm CCD focusing mirrors 2011-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8726 ESRF ID23-2
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 2 100 85.1 0.111 12.06 2.893 189394 101239 -3 17.7
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 2 2.1 84.6 0.369 3.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 structure of as-isolated hydrogenase-1 refined at 1.67A resolution 2 25 101213 101213 5076 87.61 0.1424 0.1424 0.1406 0.1506 0.1769 0.1859 RANDOM 11.328
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] 0.17 0.72 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 15.8 r_dihedral_angle_3_deg 12.771 r_dihedral_angle_1_deg 5.749 r_scangle_it 4.091 r_scbond_it 2.7 r_mcangle_it 1.695 r_angle_refined_deg 1.259 r_mcbond_it 1.067 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 15.8 r_dihedral_angle_3_deg 12.771 r_dihedral_angle_1_deg 5.749 r_scangle_it 4.091 r_scbond_it 2.7 r_mcangle_it 1.695 r_angle_refined_deg 1.259 r_mcbond_it 1.067 r_chiral_restr 0.087 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13182 Nucleic Acid Atoms Solvent Atoms 1232 Heterogen Atoms 116
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MxCuBE data collection XDS data reduction REFMAC phasing