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Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (Co-crystal)
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 7 293 17% (W/V) PEG 2000MME, 0.1M Trizma/HCl, 0.2M calcium acetate, 2%(V/V) butyraldoxime, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.052 α = 76.5 b = 103.931 β = 89.46 c = 114.189 γ = 87.55
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 90 CCD ADSC QUANTUM 210 2008-06-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0000 SPring-8 BL44B2
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 2.5 20 90.8 0.079 8.839 1.9 114706 -3
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) 2.5 2.59 83.1 0.293 2.046 1.9 10470
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 2.5 19.9 112560 5656 91.17 0.213 0.211 0.2248 0.243 0.2602 RANDOM 29.332
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] -3.31 0.16 1.58 3.9 -0.09 -0.59
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_1_deg 5.79 r_scangle_it 1.354 r_angle_refined_deg 1.139 r_scbond_it 0.855 r_mcangle_it 0.796 r_mcbond_it 0.457 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.709 r_dihedral_angle_4_deg 18.065 r_dihedral_angle_3_deg 15.418 r_dihedral_angle_1_deg 5.79 r_scangle_it 1.354 r_angle_refined_deg 1.139 r_scbond_it 0.855 r_mcangle_it 0.796 r_mcbond_it 0.457 r_nbtor_refined 0.296 r_nbd_refined 0.191 r_symmetry_vdw_refined 0.188 r_symmetry_hbond_refined 0.153 r_xyhbond_nbd_refined 0.129 r_chiral_restr 0.082 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22645 Nucleic Acid Atoms Solvent Atoms 619 Heterogen Atoms 392
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SPACE data collection HKL-2000 data reduction HKL-2000 data scaling