6B2U

Crystal structure of Xanthomonas campestris OleA H285N with Cerulenin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629215% PEG 4000, 105 MM MANGANESE CHLORIDE, 100 MM MES PH 6.0
Crystal Properties
Matthews coefficientSolvent content
2.3142.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.516α = 90
b = 90.516β = 90
c = 69.793γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.03322APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.0429.51990.0610.0640.020.99924.29.82087636.3
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)
12.042.0995.50.7730.8180.2640.7519

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 REPLACEMENTTHROUGHOUT3S212.0429.5119822104898.260.18120.17860.23RANDOM50.006
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]
-0.17-0.08-0.170.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.505
r_dihedral_angle_4_deg22.35
r_dihedral_angle_3_deg18.929
r_dihedral_angle_1_deg7.523
r_angle_refined_deg1.288
r_angle_other_deg0.673
r_chiral_restr0.082
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.505
r_dihedral_angle_4_deg22.35
r_dihedral_angle_3_deg18.929
r_dihedral_angle_1_deg7.523
r_angle_refined_deg1.288
r_angle_other_deg0.673
r_chiral_restr0.082
r_gen_planes_refined0.013
r_bond_refined_d0.011
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2509
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms9

Software

Software
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction