7DOR

E. coli GyrB ATPase domain in complex with 4-nitropheno


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
2.3447.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.811α = 90
b = 67.519β = 90
c = 102.493γ = 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 BL19U10.979SSRFBL19U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.856.3899.70.0810.0880.0346.46.539937
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8399.20.6460.710.290.8055.7

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 REPLACEMENTTHROUGHOUT5Z9B1.8956.3832328167799.060.209440.208060.23675RANDOM35.124
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]
-1.132.54-1.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.01
r_dihedral_angle_3_deg14.754
r_dihedral_angle_4_deg12.447
r_long_range_B_refined5.566
r_long_range_B_other5.558
r_scangle_other3.875
r_angle_other_deg3.784
r_mcangle_it2.8
r_mcangle_other2.799
r_dihedral_angle_1_deg2.653
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.01
r_dihedral_angle_3_deg14.754
r_dihedral_angle_4_deg12.447
r_long_range_B_refined5.566
r_long_range_B_other5.558
r_scangle_other3.875
r_angle_other_deg3.784
r_mcangle_it2.8
r_mcangle_other2.799
r_dihedral_angle_1_deg2.653
r_scbond_it2.465
r_scbond_other2.432
r_mcbond_it1.911
r_mcbond_other1.911
r_angle_refined_deg1.579
r_chiral_restr0.153
r_bond_refined_d0.023
r_gen_planes_refined0.005
r_gen_planes_other0.004
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 Atoms2885
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms40

Software

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