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Crystal Structure of Aldoxime Dehydratase (OxdRE) in Complex with Butyraldoxime (soaked 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 7.4 293 18% (W/V) PEG 4000, 0.075M sodium cacodylate, 0.1M magnesium acetate, pH 7.4, vapor diffusion, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.118 α = 90 b = 148.569 β = 90.3 c = 79.113 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 1.8 20 99.7 0.084 17.235 4.2 132895 -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) 1 1.8 1.86 98 0.288 3.3 12998
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 1.8 19.93 132702 6625 98.82 0.249 0.247 0.2469 0.28 0.2793 RANDOM 11.456
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] 0.26 0.41 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.152 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_1_deg 5.904 r_scangle_it 1.408 r_angle_refined_deg 1.112 r_scbond_it 0.949 r_mcangle_it 0.666 r_mcbond_it 0.4 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.152 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 13.621 r_dihedral_angle_1_deg 5.904 r_scangle_it 1.408 r_angle_refined_deg 1.112 r_scbond_it 0.949 r_mcangle_it 0.666 r_mcbond_it 0.4 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.235 r_symmetry_hbond_refined 0.224 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.082 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11249 Nucleic Acid Atoms Solvent Atoms 868 Heterogen Atoms 196
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