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Crystal structure of Xanthomonas campestris OleA H285N 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 15% PEG 4000, 105 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0
Crystal Properties Matthews coefficient Solvent content 2.31 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.516 α = 90 b = 90.516 β = 90 c = 69.793 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 PIXEL PSI PILATUS 6M 2015-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.04 29.51 99 0.061 0.064 0.02 0.999 24.2 9.8 20876 36.3
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 2.04 2.09 95.5 0.773 0.818 0.264 0.751 9
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 3S21 2.04 29.51 19822 1048 98.26 0.1812 0.1786 0.1912 0.23 0.2327 RANDOM 50.006
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] -0.17 -0.08 -0.17 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.505 r_dihedral_angle_4_deg 22.35 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.523 r_angle_refined_deg 1.288 r_angle_other_deg 0.673 r_chiral_restr 0.082 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.505 r_dihedral_angle_4_deg 22.35 r_dihedral_angle_3_deg 18.929 r_dihedral_angle_1_deg 7.523 r_angle_refined_deg 1.288 r_angle_other_deg 0.673 r_chiral_restr 0.082 r_gen_planes_refined 0.013 r_bond_refined_d 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2509 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 9
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing XDS data reduction