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Crystal structure of the ATP binding domain of S. aureus GyrB complexed with LMD62
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CPH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1 M HEPES/MOPS pH 7.5
0.03 M magnesium chloride
0.03 M calcium chloride
25 % v/v MPD
25% v/v PEG 1000
25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.1 40.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.7 α = 90 b = 55.36 β = 100.42 c = 50.81 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 EIGER2 XE 16M 2019-03-02 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) 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 1.7 51.5 98 0.043 0.999 15.6 5.1 42170
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 97.3 1.433 0.475 1 5.3
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 5cph 1.7 51.5 40138 2031 97.99 0.1873 0.1861 0.1991 0.2113 0.2239 RANDOM 35.721
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] -1.09 -2.98 0.67 1.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_4_deg 17.716 r_dihedral_angle_3_deg 13.413 r_dihedral_angle_1_deg 5.967 r_angle_refined_deg 1.736 r_angle_other_deg 1.364 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.775 r_dihedral_angle_4_deg 17.716 r_dihedral_angle_3_deg 13.413 r_dihedral_angle_1_deg 5.967 r_angle_refined_deg 1.736 r_angle_other_deg 1.364 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3049 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 118
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling REFMAC phasing