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Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a fragment
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, HANGING DROP 7.6 296 40-43% MPD_P1K_P3350, 100 mM Mops/Na-Hepes, 100 mM Divalents
Crystal Properties Matthews coefficient Solvent content 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.66 α = 90 b = 55.65 β = 101.01 c = 51.14 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 CCD ADSC QUANTUM 315 2010-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9763 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.45 25.858 99.3 0.141 0.169 0.091 5.5 3.3 69300 69300
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.53 99 0.48 0.48 0.305 1.4 3.3 10077
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 1.45 25.86 65826 3472 99.26 0.1776 0.1762 0.1754 0.2037 0.2038 RANDOM 12.134
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] 0.18 0.31 -0.74 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 13.013 r_dihedral_angle_1_deg 5.577 r_angle_refined_deg 2.285 r_mcangle_it 2.08 r_mcbond_it 1.356 r_mcbond_other 1.347 r_angle_other_deg 1.122 r_chiral_restr 0.136
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.561 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 13.013 r_dihedral_angle_1_deg 5.577 r_angle_refined_deg 2.285 r_mcangle_it 2.08 r_mcbond_it 1.356 r_mcbond_other 1.347 r_angle_other_deg 1.122 r_chiral_restr 0.136 r_bond_refined_d 0.021 r_gen_planes_refined 0.013 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3083 Nucleic Acid Atoms Solvent Atoms 479 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing PDB_EXTRACT data extraction