7DQJ

E. coli GyrB ATPase domain in complex with 3,4-Dihydroxyacetophenone


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
2.5752.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.46α = 90
b = 67.462β = 90
c = 102.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97853SSRFBL19U1

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
11.9256.3599.70.9822.5266.533267
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)
11.921.990.944

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 REPLACEMENTTHROUGHOUT5Z9B1.9256.3531554166199.570.236850.235480.26306RANDOM34.753
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]
0.211.54-1.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_3_deg11.311
r_dihedral_angle_4_deg8.188
r_dihedral_angle_1_deg4.818
r_angle_other_deg3.802
r_long_range_B_refined3.15
r_long_range_B_other3.083
r_mcangle_it1.44
r_mcangle_other1.44
r_scangle_other1.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.662
r_dihedral_angle_3_deg11.311
r_dihedral_angle_4_deg8.188
r_dihedral_angle_1_deg4.818
r_angle_other_deg3.802
r_long_range_B_refined3.15
r_long_range_B_other3.083
r_mcangle_it1.44
r_mcangle_other1.44
r_scangle_other1.237
r_angle_refined_deg1.048
r_mcbond_it0.811
r_mcbond_other0.811
r_scbond_it0.72
r_scbond_other0.719
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_gen_planes_other0.002
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 Atoms2861
Nucleic Acid Atoms
Solvent Atoms112
Heterogen Atoms47

Software

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