☰ Navigation Tabs
Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with sodium dithionite and sodium sulfide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VLB PDB ENTRY 1VLB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 277 VAPOR DIFFUSION, SITTING DROP, AT 277 K. CRYSTALLIZED USING 30% ISOPROPANOL, 0.2M MGCL2, 0.2M HEPES PH 7.6. ISOPROPANOL WAS REMOVED AND CRYSTALS WERE SOAKED WITH 30MM SODIUM DITHIONITE AND 7MM SODIUM SULFIDE FOR 24H.
Crystal Properties Matthews coefficient Solvent content 2.47 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.25 α = 90 b = 143.25 β = 90 c = 162.3 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 77 CCD ADSC QUANTUM 4r 2007-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 1.57 25.68 99.5 0.09 12.5 5.3 135137 2
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 1.57 1.65 99.9 0.35 3.8 4.9
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 1VLB 1.57 124.06 128341 6793 99.32 0.13557 0.1344 0.1462 0.15792 0.1667 RANDOM 15.539
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 -0.09 -0.19 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.749 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 6.45 r_scbond_it 2.391 r_angle_refined_deg 1.627 r_mcangle_it 1.606 r_mcbond_it 1.15 r_mcbond_other 1.149 r_angle_other_deg 0.855
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.749 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_3_deg 12.551 r_dihedral_angle_1_deg 6.45 r_scbond_it 2.391 r_angle_refined_deg 1.627 r_mcangle_it 1.606 r_mcbond_it 1.15 r_mcbond_other 1.149 r_angle_other_deg 0.855 r_chiral_restr 0.092 r_gen_planes_other 0.029 r_bond_other_d 0.019 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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_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 6815 Nucleic Acid Atoms Solvent Atoms 1232 Heterogen Atoms 70
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing