4PRX

E. coli GyrB 43-kDa N-terminal fragment in complex with ADP+Pi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EI1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.1M tri-ammonium citrate pH 6.5, 25%(w/v) PEG2000, vapor diffusion, sitting drop, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
2.9457.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.64α = 90
b = 131.65β = 90
c = 92.39γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-09-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0000SLSX06SA

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
11.846.1999.70.09217.184405244052-334.429
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.9198.30.9480.9943.22

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1EI11.846.19-34405244052198699.690.1650.1650.16330.2029RANDOM29.421
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]
1.73-0.98-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg17.818
r_dihedral_angle_3_deg12.413
r_dihedral_angle_1_deg5.919
r_angle_refined_deg2
r_angle_other_deg0.893
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.877
r_dihedral_angle_4_deg17.818
r_dihedral_angle_3_deg12.413
r_dihedral_angle_1_deg5.919
r_angle_refined_deg2
r_angle_other_deg0.893
r_chiral_restr0.12
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2764
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms39

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction