4LC3

X-ray crystal structure of a putative UDP-4-amino-4-deoxy-l-arabinose--oxoglutarate aminotransferase from Burkholderia cenocepacia


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MDOPDB ENTRY 1MDO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP528920% PEG6000, 100 mM sodium citrate tribasic, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.754.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 190.93α = 90
b = 58.91β = 97.39
c = 83.08γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-06-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

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
11.65097.20.06315.62120854117470-318.906
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6495.60.3713.58

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1MDO1.647.38120854117469591897.180.1130.11110.1479RANDOM14.0425
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]
-0.14-0.310.21-0.03
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.609
r_dihedral_angle_2_deg29.294
r_dihedral_angle_4_deg14.632
r_dihedral_angle_3_deg11.605
r_sphericity_bonded9.723
r_dihedral_angle_1_deg5.733
r_rigid_bond_restr2.521
r_mcangle_it1.552
r_angle_refined_deg1.407
r_mcbond_it1.286
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free33.609
r_dihedral_angle_2_deg29.294
r_dihedral_angle_4_deg14.632
r_dihedral_angle_3_deg11.605
r_sphericity_bonded9.723
r_dihedral_angle_1_deg5.733
r_rigid_bond_restr2.521
r_mcangle_it1.552
r_angle_refined_deg1.407
r_mcbond_it1.286
r_mcbond_other1.277
r_angle_other_deg0.811
r_chiral_restr0.16
r_bond_refined_d0.011
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5774
Nucleic Acid Atoms
Solvent Atoms1016
Heterogen Atoms74

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction