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Structure of the Oxidized Unready Form of Ni-Fe Hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FRF PDB ENTRY 1FRF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 PEG 6000, glycerol, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.41 α = 90 b = 99.7 β = 91.42 c = 182.83 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 100 CCD MARRESEARCH mirrors 1998-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954 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 1.83 35 83.1 0.054 11.8 3.06 169544 169544 3 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.88 68.5 0.255 2.5 3.01
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 PDB ENTRY 1FRF 1.83 20 168613 160130 8483 83.01 0.14821 0.14821 0.14628 0.1609 0.18467 0.1899 RANDOM 11.791
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] 2.89 1.18 -0.86 -1.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.021 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 5.499 r_scangle_it 3.512 r_scbond_it 2.699 r_mcangle_it 2.082 r_mcbond_it 1.646 r_angle_refined_deg 1.156 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.021 r_dihedral_angle_4_deg 17.243 r_dihedral_angle_3_deg 14.446 r_dihedral_angle_1_deg 5.499 r_scangle_it 3.512 r_scbond_it 2.699 r_mcangle_it 2.082 r_mcbond_it 1.646 r_angle_refined_deg 1.156 r_nbtor_refined 0.312 r_nbd_refined 0.21 r_symmetry_vdw_refined 0.195 r_symmetry_hbond_refined 0.159 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.08 r_bond_refined_d 0.01 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 18394 Nucleic Acid Atoms Solvent Atoms 1848 Heterogen Atoms 211
Software Software Software Name Purpose XDS data scaling CCP4 data reduction AMoRE phasing REFMAC refinement ProDC data collection CCP4 data scaling