3KGF

The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529120mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005%(v/v) Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
3.9568.84

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.537α = 90
b = 204.537β = 90
c = 66.462γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATERIGAKU RAXIS IVOsmic Blue Mirrors2005-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.542

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
1239.598.20.0648.22.0710542510542537.5
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)
122.0787.20.3812.12.3810487

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 REPLACEMENTTHROUGHOUT2b7o232.67105110105110524597.910.164230.1640.1630.191RANDOM25.418
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]
-0.15-0.08-0.150.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.003
r_dihedral_angle_4_deg15.749
r_dihedral_angle_3_deg12.893
r_dihedral_angle_1_deg6.187
r_scangle_it4.212
r_scbond_it2.796
r_angle_refined_deg1.318
r_mcangle_it1.09
r_angle_other_deg0.976
r_mcbond_it0.696
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.003
r_dihedral_angle_4_deg15.749
r_dihedral_angle_3_deg12.893
r_dihedral_angle_1_deg6.187
r_scangle_it4.212
r_scbond_it2.796
r_angle_refined_deg1.318
r_mcangle_it1.09
r_angle_other_deg0.976
r_mcbond_it0.696
r_symmetry_vdw_other0.269
r_nbd_refined0.204
r_nbd_other0.203
r_nbtor_refined0.164
r_xyhbond_nbd_refined0.163
r_symmetry_hbond_refined0.163
r_mcbond_other0.161
r_symmetry_vdw_refined0.101
r_nbtor_other0.083
r_chiral_restr0.074
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6976
Nucleic Acid Atoms
Solvent Atoms771
Heterogen Atoms191

Software

Software
Software NamePurpose
CrystalCleardata collection
CCP4model building
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing