5Z9B

Bacterial GyrB ATPase domain in complex with (3,4-dichlorophenyl)hydrazine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DUH 

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
2.3848.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.782α = 90
b = 68.231β = 90
c = 102.529γ = 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
12.156.8197.60.07831.64.525391
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)
12.12.181000.2354.7

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 REPLACEMENTTHROUGHOUT4DUH2.156.824072125197.080.20180.200560.2263RANDOM26.057
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]
0.77-0.35-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.871
r_dihedral_angle_3_deg14.251
r_dihedral_angle_4_deg14.224
r_dihedral_angle_1_deg5.32
r_long_range_B_refined4.407
r_long_range_B_other4.407
r_scangle_other2.62
r_mcangle_it2.043
r_mcangle_other2.043
r_scbond_it1.615
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.871
r_dihedral_angle_3_deg14.251
r_dihedral_angle_4_deg14.224
r_dihedral_angle_1_deg5.32
r_long_range_B_refined4.407
r_long_range_B_other4.407
r_scangle_other2.62
r_mcangle_it2.043
r_mcangle_other2.043
r_scbond_it1.615
r_scbond_other1.615
r_angle_refined_deg1.338
r_mcbond_it1.201
r_mcbond_other1.201
r_angle_other_deg0.999
r_chiral_restr0.074
r_bond_refined_d0.008
r_bond_other_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.002
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 Atoms2870
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms50

Software

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