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Structure of the unready oxidized form of [NiFe] hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FRV PDB ENTRY 2FRV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 293 PEG8000, sodium chloride, N,N-dimethyl dodecylamine N-oxide, glycerol, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.30
Crystal Properties Matthews coefficient Solvent content 2.3 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.75 α = 89.33 b = 93.44 β = 102.41 c = 69.03 γ = 90.95
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH 1996-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.35 19.8 86.2 0.069 8.4 1.8 58639 37.6
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 2.35 2.45 78.2
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 2FRV 2.35 13 61447 58485 2962 92.2 0.135 0.132 0.1503 0.183 0.1976 RANDOM 14.54
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] 2.37 -1.11 0.02 0.13 0.9 -2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 17.933 r_dihedral_angle_1_deg 5.397 r_scangle_it 2.52 r_scbond_it 1.969 r_mcangle_it 1.473 r_mcbond_it 1.157 r_angle_refined_deg 1.088 r_nbtor_refined 0.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.337 r_dihedral_angle_4_deg 19.189 r_dihedral_angle_3_deg 17.933 r_dihedral_angle_1_deg 5.397 r_scangle_it 2.52 r_scbond_it 1.969 r_mcangle_it 1.473 r_mcbond_it 1.157 r_angle_refined_deg 1.088 r_nbtor_refined 0.324 r_symmetry_hbond_refined 0.282 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.158 r_symmetry_vdw_refined 0.158 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 12237 Nucleic Acid Atoms Solvent Atoms 515 Heterogen Atoms 114
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ProDC data collection XDS data scaling AMoRE phasing