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Glycerol inhibited form of Aldehyde oxidoreductase from Desulfovibrio gigas
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 277 isopropanol, MgCl2, pH 7.6, vapor diffusion, sitting drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.44 49.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.56 α = 90 b = 142.56 β = 90 c = 161.88 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 210 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.72 123.09 99.2 0.086 0.086 6.158 4 101724
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.72 1.81 99.8 0.446 0.446 1.7 3.9 14763
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 1VLB 1.72 26.98 101625 5078 98.97 0.161 0.16 0.1903 0.191 0.2132 RANDOM 26.097
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] 0.19 0.1 0.19 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_3_deg 12.267 r_sphericity_free 9.818 r_dihedral_angle_1_deg 6.484 r_sphericity_bonded 3.862 r_rigid_bond_restr 2.639 r_scangle_it 2.602 r_scbond_it 1.677 r_angle_refined_deg 1.458
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.564 r_dihedral_angle_4_deg 15.491 r_dihedral_angle_3_deg 12.267 r_sphericity_free 9.818 r_dihedral_angle_1_deg 6.484 r_sphericity_bonded 3.862 r_rigid_bond_restr 2.639 r_scangle_it 2.602 r_scbond_it 1.677 r_angle_refined_deg 1.458 r_mcangle_it 0.903 r_mcbond_it 0.597 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.113 r_chiral_restr 0.11 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6814 Nucleic Acid Atoms Solvent Atoms 1108 Heterogen Atoms 79
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction