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E.coli GyrB24 with inhibitor KOB20 (EBL2583)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KZN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 41.7% w/v PEG4000,80 mM MgCl2,100 mM Tris pH8,1 mM KOB20,4.6% DMSO
Crystal Properties Matthews coefficient Solvent content 2.03 39.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.17 α = 90 b = 49.77 β = 102.11 c = 53.04 γ = 90
Symmetry Space Group C 1 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 DECTRIS EIGER X 16M 2019-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.6 51.86 99.8 0.062 0.067 0.025 0.999 13.5 6.8 25698
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 1.6 1.63 99.1 1.215 1.321 0.512 0.684 6.5
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 1kzn 1.6 51.86 24091 1269 98.42 0.1447 0.1418 0.1446 0.1988 0.203 RANDOM 30.05
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] 1.31 -1.06 -2.2 1.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.125 r_dihedral_angle_3_deg 13.226 r_dihedral_angle_4_deg 10.541 r_dihedral_angle_1_deg 6.31 r_rigid_bond_restr 2.264 r_angle_refined_deg 1.448 r_angle_other_deg 1.357 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.125 r_dihedral_angle_3_deg 13.226 r_dihedral_angle_4_deg 10.541 r_dihedral_angle_1_deg 6.31 r_rigid_bond_restr 2.264 r_angle_refined_deg 1.448 r_angle_other_deg 1.357 r_chiral_restr 0.068 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1496 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 34
Software Software Software Name Purpose XDS data reduction Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction REFMAC phasing