3U0E

Crystal structure of beta-ketoacyl synthase from Brucella melitensis in complex with fragment 9320


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LRFnative structure 3lrf

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE, CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL, BrabA.00113.a.A1.PW25441 AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.2545.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.07α = 90
b = 83.75β = 121.5
c = 73.61γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2009-09-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97740ALS5.0.1

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
11.65099.40.04522.574.45337153077-318.91
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6497.20.220.225.553.53843

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTnative structure 3lrf1.620533715307727130.1380.1380.1370.156RANDOM13.36
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]
-0.12-0.120.18-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.394
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg11.796
r_dihedral_angle_1_deg6.281
r_angle_refined_deg1.589
r_angle_other_deg0.968
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.394
r_dihedral_angle_4_deg15.555
r_dihedral_angle_3_deg11.796
r_dihedral_angle_1_deg6.281
r_angle_refined_deg1.589
r_angle_other_deg0.968
r_chiral_restr0.094
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3020
Nucleic Acid Atoms
Solvent Atoms471
Heterogen Atoms15

Software

Software
Software NamePurpose
BOSdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling