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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 2.09 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 142.892 α = 90 b = 55.655 β = 100.55 c = 51.213 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 IMAGE PLATE RIGAKU RAXIS IV++ 2010-08-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 45.01 98.8 0.046 10.4 2.27 51605
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 98.4 0.297 2.3 2.19 5057
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 45.01 48976 2623 98.74 0.1867 0.1849 0.1978 0.2195 0.2271 RANDOM 26.594
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 -0.08 -0.55 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.414 r_dihedral_angle_4_deg 20.714 r_dihedral_angle_3_deg 13.111 r_dihedral_angle_1_deg 5.588 r_mcangle_it 3.368 r_mcbond_it 2.263 r_mcbond_other 2.262 r_angle_refined_deg 2.047 r_angle_other_deg 1.044 r_chiral_restr 0.116
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.414 r_dihedral_angle_4_deg 20.714 r_dihedral_angle_3_deg 13.111 r_dihedral_angle_1_deg 5.588 r_mcangle_it 3.368 r_mcbond_it 2.263 r_mcbond_other 2.262 r_angle_refined_deg 2.047 r_angle_other_deg 1.044 r_chiral_restr 0.116 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3072 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement d*TREK data reduction d*TREK data scaling MOLREP phasing PDB_EXTRACT data extraction