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Crystal structure of Xanthomonas campestris OleA E117D bound with Cerulenin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S21
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 292 12% PEG 4000, 70 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.24 45.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.765 α = 90 b = 89.765 β = 90 c = 69.509 γ = 120
Symmetry Space Group P 32 2 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 210r 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 1.02235 APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.08 50 98.8 0.143 0.151 0.047 11.8 10.3 19937 36.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.08 2.12 100 0.72 0.759 0.237 0.746 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 FOURIER SYNTHESIS THROUGHOUT 3S21 2.08 50 18913 1004 98.53 0.1741 0.1711 0.1824 0.2289 0.2282 RANDOM 48.522
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] -0.31 -0.16 -0.31 1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 2.306 r_angle_other_deg 1.164 r_chiral_restr 0.134 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.948 r_dihedral_angle_4_deg 19.472 r_dihedral_angle_3_deg 16.634 r_dihedral_angle_1_deg 6.777 r_angle_refined_deg 2.306 r_angle_other_deg 1.164 r_chiral_restr 0.134 r_bond_refined_d 0.025 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2534 Nucleic Acid Atoms Solvent Atoms 45 Heterogen Atoms 17
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing HKL-2000 data scaling