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Structure of 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 6.4 293 VAPOR DIFFUSION, PH 6.4, 293 K, PEG6000, MES, IN A GLOVEBOX
Crystal Properties Matthews coefficient Solvent content 2.2 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.01 α = 90 b = 100.17 β = 91.42 c = 183.98 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 CCD 2000-04-24 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 2.3 30 88.7 0.06 12.7 3.1 92983
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 2.3 2.36 52.9 0.2 3.7 1.4
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 2.3 25 88317 4628 88.65 0.17475 0.17308 0.1761 0.20688 0.2109 RANDOM 37.384
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] 4.46 1.83 -2.12 -2.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 4.064 r_mcangle_it 3.564 r_scbond_it 3.388 r_mcbond_it 2.581 r_angle_refined_deg 1.252 r_chiral_restr 0.084 r_bond_refined_d 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.184 r_dihedral_angle_4_deg 15.013 r_dihedral_angle_3_deg 12.696 r_dihedral_angle_1_deg 4.064 r_mcangle_it 3.564 r_scbond_it 3.388 r_mcbond_it 2.581 r_angle_refined_deg 1.252 r_chiral_restr 0.084 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 18396 Nucleic Acid Atoms Solvent Atoms 982 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing