3LLS

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FTPPDB entry 3FTP modified with CCP4 program CHAINSAW

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52901.5M AMMONIUM SULPHATE, 100MM HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.4950.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.37α = 90
b = 101.37β = 90
c = 165.18γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2009-12-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.45099.30.1050.10513.545.73911338839-339.4
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)
12.42.4699.50.570.573.175.42847

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 REPLACEMENTTHROUGHOUTPDB entry 3FTP modified with CCP4 program CHAINSAW2.4203911338769194099.30.1840.1840.1820.228RANDOM10.78
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]
0.690.350.69-1.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.965
r_dihedral_angle_4_deg16.618
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.179
r_scangle_it3.141
r_scbond_it1.935
r_angle_refined_deg1.449
r_mcangle_it1.021
r_angle_other_deg0.865
r_mcbond_it0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.965
r_dihedral_angle_4_deg16.618
r_dihedral_angle_3_deg13.009
r_dihedral_angle_1_deg6.179
r_scangle_it3.141
r_scbond_it1.935
r_angle_refined_deg1.449
r_mcangle_it1.021
r_angle_other_deg0.865
r_mcbond_it0.56
r_mcbond_other0.149
r_chiral_restr0.079
r_bond_refined_d0.015
r_gen_planes_refined0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5728
Nucleic Acid Atoms
Solvent Atoms395
Heterogen Atoms53

Software

Software
Software NamePurpose
StructureStudiodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling