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Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with benzaldehyde
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 CRYSTAL WAS SOAKED WITH 1.4MM BENZALDEHYDE FOR 1H.
Crystal Properties Matthews coefficient Solvent content 2.47 50.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.229 α = 90 b = 143.229 β = 90 c = 162.25 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 PIXEL DECTRIS PILATUS 6M 2011-11-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 1.49 124.04 99.7 0.04 20.4 5.7 158222 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 1.49 1.52 100 0.22 7 6.5
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 1.49 124.04 150228 7930 99.63 0.09264 0.09109 0.1116 0.12215 0.1362 RANDOM 14.121
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_sphericity_free 38.613 r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 16.254 r_dihedral_angle_3_deg 11.756 r_sphericity_bonded 10.072 r_dihedral_angle_1_deg 6.456 r_rigid_bond_restr 2.59 r_angle_refined_deg 1.999 r_scbond_it 1.699 r_mcangle_it 1.538
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 38.613 r_dihedral_angle_2_deg 35.902 r_dihedral_angle_4_deg 16.254 r_dihedral_angle_3_deg 11.756 r_sphericity_bonded 10.072 r_dihedral_angle_1_deg 6.456 r_rigid_bond_restr 2.59 r_angle_refined_deg 1.999 r_scbond_it 1.699 r_mcangle_it 1.538 r_mcbond_it 1.123 r_mcbond_other 1.122 r_angle_other_deg 0.913 r_chiral_restr 0.096 r_gen_planes_other 0.023 r_bond_other_d 0.014 r_bond_refined_d 0.012 r_gen_planes_refined 0.012 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6815 Nucleic Acid Atoms Solvent Atoms 1270 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction Aimless data scaling PHASER phasing