3N74

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Brucella melitensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CGO 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP928940.4 mg/mL protein against PACT screen condition d6, 0.1 M MMT buffer pH 9, 25% PEG 1500, 25% ethylene glycol used as cryo-protectant, crystal tracking ID 205370d6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0439.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.52α = 90
b = 96.5β = 90
c = 130.34γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

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
12.25099.90.14713.397.24590045847-324.798
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)
2.22.2699.60.5084.973367

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 REPLACEMENTTHROUGHOUT1cgo2.25045664230199.480.1730.170.23RANDOM17.105
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]
0.131.03-1.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.158
r_dihedral_angle_4_deg16.826
r_dihedral_angle_3_deg14.063
r_dihedral_angle_1_deg5.497
r_scangle_it3.692
r_scbond_it2.189
r_angle_refined_deg1.356
r_mcangle_it1.138
r_mcbond_it0.613
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.158
r_dihedral_angle_4_deg16.826
r_dihedral_angle_3_deg14.063
r_dihedral_angle_1_deg5.497
r_scangle_it3.692
r_scbond_it2.189
r_angle_refined_deg1.356
r_mcangle_it1.138
r_mcbond_it0.613
r_chiral_restr0.087
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6531
Nucleic Acid Atoms
Solvent Atoms593
Heterogen Atoms

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction