5Z9Q

Bacterial GyrB ATPase domain in complex with a chemical fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2810.1M Tris-HCl pH 7.5, 2.20M (NH4)2HPO4, 10mM 2-aminobenzimidazole
Crystal Properties
Matthews coefficientSolvent content
2.3647.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.922α = 90
b = 68.728β = 90
c = 102.345γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-07-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7557.0689.50.0647.35.439606
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8181.30.3087.25.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4DUH1.857.0634845178690.30.209650.208650.22949RANDOM26.64
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]
0.111.01-1.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.253
r_dihedral_angle_4_deg12.308
r_dihedral_angle_3_deg12.251
r_dihedral_angle_1_deg5.293
r_long_range_B_refined4.357
r_long_range_B_other4.356
r_scangle_other2.148
r_mcangle_it1.987
r_mcangle_other1.986
r_angle_refined_deg1.281
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.253
r_dihedral_angle_4_deg12.308
r_dihedral_angle_3_deg12.251
r_dihedral_angle_1_deg5.293
r_long_range_B_refined4.357
r_long_range_B_other4.356
r_scangle_other2.148
r_mcangle_it1.987
r_mcangle_other1.986
r_angle_refined_deg1.281
r_scbond_it1.275
r_scbond_other1.275
r_mcbond_it1.151
r_mcbond_other1.151
r_angle_other_deg0.927
r_chiral_restr0.075
r_bond_refined_d0.007
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2800
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALAdata scaling
MOLREPphasing