5VXI

Crystal structure of Xanthomonas campestris OleA E117D bound with Cerulenin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S21 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629212% PEG 4000, 70 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.2445.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.765α = 90
b = 89.765β = 90
c = 69.509γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2017-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM1.02235APS19-BM

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
12.085098.80.1430.1510.04711.810.31993736.1
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)
12.082.121000.720.7590.2370.74610

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT3S212.085018913100498.530.17410.17110.2289RANDOM48.522
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]
-0.31-0.16-0.311.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg19.472
r_dihedral_angle_3_deg16.634
r_dihedral_angle_1_deg6.777
r_angle_refined_deg2.306
r_angle_other_deg1.164
r_chiral_restr0.134
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.948
r_dihedral_angle_4_deg19.472
r_dihedral_angle_3_deg16.634
r_dihedral_angle_1_deg6.777
r_angle_refined_deg2.306
r_angle_other_deg1.164
r_chiral_restr0.134
r_bond_refined_d0.025
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2534
Nucleic Acid Atoms
Solvent Atoms45
Heterogen Atoms17

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing
HKL-2000data scaling