☰ Navigation Tabs
Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand
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 40.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.3 α = 90 b = 55.446 β = 100.95 c = 51.029 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++ 2011-02-03 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 50.1 98.5 0.036 12 2.68 51220
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 90.3 0.492 2.2 2.44 4646
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KZN 1.6 50.1 48608 2607 98.52 0.1669 0.1654 0.1946 0.211 RANDOM 29.55
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] -0.07 -0.43 -0.04 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.949 r_dihedral_angle_4_deg 18.186 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_1_deg 6.358 r_mcangle_it 3.322 r_angle_refined_deg 2.527 r_mcbond_it 2.237 r_mcbond_other 2.22 r_angle_other_deg 1.189 r_chiral_restr 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.949 r_dihedral_angle_4_deg 18.186 r_dihedral_angle_3_deg 15.582 r_dihedral_angle_1_deg 6.358 r_mcangle_it 3.322 r_angle_refined_deg 2.527 r_mcbond_it 2.237 r_mcbond_other 2.22 r_angle_other_deg 1.189 r_chiral_restr 0.147 r_bond_refined_d 0.026 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 3076 Nucleic Acid Atoms Solvent Atoms 292 Heterogen Atoms 89
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling MOLREP phasing PDB_EXTRACT data extraction d*TREK data reduction