7DQI

E. coli GyrB ATPase domain in complex with Esculetin


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
2.3752.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.862α = 90
b = 67.601β = 90
c = 102.79γ = 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
11.9156.4896.80.99826.3246.733058
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)
11.911.980.7

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 REPLACEMENTTHROUGHOUT5Z9B1.9156.4831409161596.850.238270.237630.25041RANDOM31.415
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]
0.010.03-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.889
r_dihedral_angle_3_deg9.848
r_dihedral_angle_4_deg8.089
r_dihedral_angle_1_deg4.756
r_long_range_B_refined4.594
r_angle_other_deg3.814
r_long_range_B_other2.891
r_mcangle_it1.356
r_mcangle_other1.356
r_scangle_other1.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.889
r_dihedral_angle_3_deg9.848
r_dihedral_angle_4_deg8.089
r_dihedral_angle_1_deg4.756
r_long_range_B_refined4.594
r_angle_other_deg3.814
r_long_range_B_other2.891
r_mcangle_it1.356
r_mcangle_other1.356
r_scangle_other1.083
r_angle_refined_deg1.065
r_mcbond_it0.751
r_mcbond_other0.751
r_scbond_it0.618
r_scbond_other0.616
r_chiral_restr0.064
r_bond_refined_d0.007
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 Atoms2858
Nucleic Acid Atoms
Solvent Atoms142
Heterogen Atoms46

Software

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