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The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BOJ PDB ENTRY 2BOJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283 50% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K
Crystal Properties Matthews coefficient Solvent content 2.57 52.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.93 α = 90 b = 95.93 β = 90 c = 165.81 γ = 90
Symmetry Space Group I 41 2 2
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 mirrors 2007-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99198 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.7 30 0.904 0.067 0.055 16.92 5.3 35596 35596
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 1.7 1.8 0.71 0.5 3 3.7
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 (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 2BOJ 1.75 10 35571 35596 1886 95.93 0.1815 0.17943 0.1788 0.21994 0.2178 RANDOM 31.601
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] 0.8 0.8 -1.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.374 r_dihedral_angle_4_deg 22.314 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 5.246 r_scangle_it 4.068 r_scbond_it 2.622 r_angle_refined_deg 1.727 r_mcangle_it 1.5 r_mcbond_it 1.038 r_symmetry_hbond_refined 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.374 r_dihedral_angle_4_deg 22.314 r_dihedral_angle_3_deg 13.75 r_dihedral_angle_1_deg 5.246 r_scangle_it 4.068 r_scbond_it 2.622 r_angle_refined_deg 1.727 r_mcangle_it 1.5 r_mcbond_it 1.038 r_symmetry_hbond_refined 0.335 r_nbtor_refined 0.305 r_nbd_refined 0.212 r_chiral_restr 0.2 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2591 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XDS data scaling EPMR phasing