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Crystal structure of the ATP binding domain of S. aureus GyrB complexed with ULD-2
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 6.5 293.15 0.1 M imidazole/MES pH 6.5, 0.06 M divalent cations (0.03 M magnesium chloride, 0.03 M calcium chloride), 37.5 % precipitant mix 4 (25 % v/v MPD, 25% v/v PEG 1000, 25% w/v PEG 3350)
Crystal Properties Matthews coefficient Solvent content 2.08 40.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.594 α = 90 b = 55.429 β = 101 c = 50.976 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 PILATUS 6M 2019-06-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.0332 PETRA III, EMBL c/o DESY P13 (MX1)
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 45.06 99.4 0.069 0.077 0.033 0.998 10.2 5.1 51937
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 91.8 1.336 1.49 0.645 0.448 4.8
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 1.6 37.59 49335 2598 99.42 0.1784 0.1772 0.1886 0.1998 0.2122 RANDOM 30.151
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] 0.1 -0.23 -0.48 0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_3_deg 13.217 r_dihedral_angle_4_deg 13.038 r_dihedral_angle_1_deg 5.848 r_angle_refined_deg 1.839 r_angle_other_deg 1.38 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.765 r_dihedral_angle_3_deg 13.217 r_dihedral_angle_4_deg 13.038 r_dihedral_angle_1_deg 5.848 r_angle_refined_deg 1.839 r_angle_other_deg 1.38 r_chiral_restr 0.069 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3036 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 120
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PDB_EXTRACT data extraction REFMAC phasing