7DQH

E. coli GyrB ATPase domain in complex with 2-hydroxybenzamide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5Z9B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2980.1 M Tris-HCl pH 7.5, 2.20 M (NH4)2HPO4, 10 mM 2-aminobenzimidazole
Crystal Properties
Matthews coefficientSolvent content
2.5852.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.517α = 90
b = 67.646β = 90
c = 102.28γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97907SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.9156.4299.80.96530.3496.433972
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.030.888

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 REPLACEMENTTHROUGHOUT5Z9B1.9156.4232261165899.550.20250.200790.23445RANDOM37.156
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]
0.033.03-3.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.387
r_dihedral_angle_4_deg15.963
r_dihedral_angle_3_deg14.115
r_long_range_B_other8.606
r_long_range_B_refined8.596
r_scangle_other7.105
r_dihedral_angle_1_deg5.692
r_scbond_it5.332
r_scbond_other5.311
r_mcangle_it5.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.387
r_dihedral_angle_4_deg15.963
r_dihedral_angle_3_deg14.115
r_long_range_B_other8.606
r_long_range_B_refined8.596
r_scangle_other7.105
r_dihedral_angle_1_deg5.692
r_scbond_it5.332
r_scbond_other5.311
r_mcangle_it5.094
r_mcangle_other5.094
r_mcbond_it4.172
r_mcbond_other4.17
r_angle_other_deg3.811
r_angle_refined_deg1.996
r_chiral_restr0.14
r_bond_refined_d0.024
r_gen_planes_other0.012
r_gen_planes_refined0.011
r_bond_other_d
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 Atoms2875
Nucleic Acid Atoms
Solvent Atoms162
Heterogen Atoms45

Software

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