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Structure of H2-treated anaerobically purified D. fructosovorans 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 VAPOR DIFFUSION, HANGING DROP 6.3 INSIDE GLOVE ANAEROBIC BOX, PEG6000, MES, PH 6.3
Crystal Properties Matthews coefficient Solvent content 2.2 44.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.77 α = 90 b = 100.4 β = 91.55 c = 183.43 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 ADSC QUANTUM 4 2001-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.08 22 87.7 0.04 15.1 3.1 123504
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 2.08 2.11 57.7 0.14 5.7 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.08 21.98 117248 6255 87.64 0.19677 0.19475 0.1954 0.23499 0.2353 RANDOM 32.876
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] 2.44 1.67 -0.28 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.737 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.32 r_mcangle_it 0.718 r_scbond_it 0.571 r_mcbond_it 0.418 r_chiral_restr 0.088 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.737 r_dihedral_angle_4_deg 16.261 r_dihedral_angle_3_deg 14.958 r_dihedral_angle_1_deg 5.81 r_angle_refined_deg 1.32 r_mcangle_it 0.718 r_scbond_it 0.571 r_mcbond_it 0.418 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18409 Nucleic Acid Atoms Solvent Atoms 1701 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing