3MQD

Crystal structure of beta-ketoacyl synthase from brucella melitensis with FOL 0758, (1-methyl-1h-indazol-3-yl) methanol


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5290MD 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 AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K
Crystal Properties
Matthews coefficientSolvent content
2.2545.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.07α = 90
b = 83.62β = 121.37
c = 73.64γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM Q315R2010-04-02SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.1ALS5.0.1

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
11.25418199.70.09112.07111226-313.34
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)
11.251.2899.10.4044

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 DIFFRACTIONMRTHROUGHOUTnative structure, 3LRF1.2541.81111141556299.80.1130.1120.133RANDOM7.42
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]
0.040.19-0.030.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.148
r_dihedral_angle_4_deg15.929
r_dihedral_angle_3_deg11.459
r_dihedral_angle_1_deg6.464
r_scangle_it5.373
r_scbond_it3.772
r_mcangle_it2.535
r_mcbond_other2.414
r_mcbond_it1.777
r_rigid_bond_restr1.735
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.148
r_dihedral_angle_4_deg15.929
r_dihedral_angle_3_deg11.459
r_dihedral_angle_1_deg6.464
r_scangle_it5.373
r_scbond_it3.772
r_mcangle_it2.535
r_mcbond_other2.414
r_mcbond_it1.777
r_rigid_bond_restr1.735
r_angle_refined_deg1.693
r_angle_other_deg1.315
r_chiral_restr0.119
r_bond_refined_d0.018
r_gen_planes_refined0.01
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_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3012
Nucleic Acid Atoms
Solvent Atoms454
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling