5VXE

Crystal structure of Xanthomonas campestris OleA E117A 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 DROP629213% PEG 4000, 100 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.2641.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.965α = 90
b = 89.965β = 90
c = 69.577γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2015-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03317APS23-ID-B

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
11.665099.30.0770.0850.03510.75.63859521.7
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)
11.661.69990.8650.9540.3980.6942.075.6

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 REPLACEMENTTHROUGHOUT3S211.665036667192599.210.17590.17410.2096RANDOM34.301
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]
-0.06-0.03-0.060.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.314
r_dihedral_angle_4_deg22.366
r_dihedral_angle_3_deg16.445
r_dihedral_angle_1_deg6.988
r_angle_refined_deg2.757
r_angle_other_deg1.29
r_chiral_restr0.164
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_gen_planes_other0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.314
r_dihedral_angle_4_deg22.366
r_dihedral_angle_3_deg16.445
r_dihedral_angle_1_deg6.988
r_angle_refined_deg2.757
r_angle_other_deg1.29
r_chiral_restr0.164
r_bond_refined_d0.031
r_gen_planes_refined0.014
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2517
Nucleic Acid Atoms
Solvent Atoms109
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKLdata scaling
HKL-2000data reduction