4PU9

E. coli GyrB 43-kDa N-terminal fragment in complex with ADP-BeF3


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.150.2M NaF, 0.1M Bis-Tris propane pH 6.5 and 20%(w/v) PEG3350, vapor diffusion, sitting drop, temperature 293.15K
Crystal Properties
Matthews coefficientSolvent content
3.0559.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.083α = 90
b = 143.245β = 90
c = 79.895γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2013-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA0.97932SLSX06DA

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
12.479.9299.70.07616.66.92013820138-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.4999.60.3850.1544.97.12086

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 REPLACEMENTTHROUGHOUT1EI12.444.08-31999119991102299.20.22170.22170.21890.2733RANDOM41.852
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]
-4.516.71-2.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.715
r_dihedral_angle_3_deg18.73
r_dihedral_angle_4_deg18.474
r_dihedral_angle_1_deg6.758
r_angle_refined_deg1.961
r_angle_other_deg0.901
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.715
r_dihedral_angle_3_deg18.73
r_dihedral_angle_4_deg18.474
r_dihedral_angle_1_deg6.758
r_angle_refined_deg1.961
r_angle_other_deg0.901
r_chiral_restr0.106
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2890
Nucleic Acid Atoms
Solvent Atoms48
Heterogen Atoms32

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction