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Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Propionaldoxime
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A15 PDB ENTRY 3A15
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 18% (W/V) PEG 4000, 0.075M sodium cacodylate, 0.1M magnesium acetate; crystal was soaked into propionaldoxime, pH 7.4, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.17 43.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.71 α = 90 b = 147.67 β = 90.008 c = 78.91 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 QUANTUM 315 2008-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 1.6 20 99.9 0.08 23.4 10 188090 -3 22.651
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) 1.6 1.64 100 0.347 8.1 10
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 3A15 1.6 19.81 188090 9497 99.93 0.25 0.248 0.2557 0.274 0.2805 RANDOM 10.508
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] 2.07 -0.22 -1.47 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.586 r_dihedral_angle_4_deg 16.804 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_1_deg 6.021 r_scangle_it 1.688 r_scbond_it 1.228 r_angle_refined_deg 1.203 r_mcangle_it 0.762 r_mcbond_it 0.5 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.586 r_dihedral_angle_4_deg 16.804 r_dihedral_angle_3_deg 13.454 r_dihedral_angle_1_deg 6.021 r_scangle_it 1.688 r_scbond_it 1.228 r_angle_refined_deg 1.203 r_mcangle_it 0.762 r_mcbond_it 0.5 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.189 r_symmetry_hbond_refined 0.163 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11674 Nucleic Acid Atoms Solvent Atoms 831 Heterogen Atoms 194
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction