5EX4

3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with tryptophan in all three allosteric binding sites


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7OPDB entry 2B7O

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M TRIS-HCL, PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL, 1 MILLIM L-TRYPTOPHAN
Crystal Properties
Matthews coefficientSolvent content
3.9869.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.68α = 90
b = 204.68β = 90
c = 66.74γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAUSTRALIAN SYNCHROTRON BEAMLINE MX20.935700Australian SynchrotronMX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
12.2544.241000.1250.1310.0414.210.87606676066
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.252.371000.3720.3720.12210.511047

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 REPLACEMENTTHROUGHOUTPDB entry 2B7O2.2544.2472258378899.990.14210.14060.1703RANDOM26.286
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]
0.390.39-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.364
r_dihedral_angle_4_deg17.413
r_dihedral_angle_3_deg13.415
r_dihedral_angle_1_deg5.944
r_mcangle_it4.641
r_mcbond_it3.15
r_mcbond_other3.147
r_angle_refined_deg1.376
r_angle_other_deg0.73
r_chiral_restr0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.364
r_dihedral_angle_4_deg17.413
r_dihedral_angle_3_deg13.415
r_dihedral_angle_1_deg5.944
r_mcangle_it4.641
r_mcbond_it3.15
r_mcbond_other3.147
r_angle_refined_deg1.376
r_angle_other_deg0.73
r_chiral_restr0.09
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7088
Nucleic Acid Atoms
Solvent Atoms707
Heterogen Atoms128

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction