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Aldehyde Oxidoreductase from Desulfovibrio gigas (MOP), soaked with 3- phenylpropionaldehyde
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 1MM 3-PHENYLPROPIONALDEHYDE FOR 1H.
Crystal Properties Matthews coefficient Solvent content 2.52 51.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.766 α = 90 b = 143.766 β = 90 c = 162.544 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 315r 2012-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.4 124.51 99.9 0.05 26.1 11.1 192977 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 1.4 1.42 97.4 0.19 9.8 10.6
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 1.4 124.51 183064 9694 99.8 0.09462 0.09343 0.1119 0.11696 0.1304 RANDOM 11.161
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] 0.02 0.01 0.02 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_sphericity_free 34.658 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 11.496 r_sphericity_bonded 8.34 r_dihedral_angle_1_deg 6.808 r_rigid_bond_restr 2.192 r_angle_refined_deg 2.007 r_scbond_it 1.258 r_mcangle_it 1.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.278 r_sphericity_free 34.658 r_dihedral_angle_4_deg 16.536 r_dihedral_angle_3_deg 11.496 r_sphericity_bonded 8.34 r_dihedral_angle_1_deg 6.808 r_rigid_bond_restr 2.192 r_angle_refined_deg 2.007 r_scbond_it 1.258 r_mcangle_it 1.173 r_angle_other_deg 0.992 r_mcbond_it 0.853 r_mcbond_other 0.853 r_chiral_restr 0.094 r_gen_planes_other 0.02 r_bond_other_d 0.014 r_gen_planes_refined 0.013 r_bond_refined_d 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 1360 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing