3RZI

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B7O2B7O, 3KGF
experimental modelPDB 3KGF2B7O, 3KGF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829320MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 8.0, 0.1MM Trp and Phe ligands, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal Properties
Matthews coefficientSolvent content
4.1170.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 207.56α = 90
b = 207.56β = 90
c = 66.977γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IV++AXCo PX70 capillary optic2010-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

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
11.9531.8899.20.0848.73.96119335
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)
11.952.0295.50.4422.32.9811440

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT2B7O, 3KGF1.9531.88113806603499.490.15360.15360.15290.168RANDOM33.9347
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]
-0.29-0.290.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg18.167
r_dihedral_angle_3_deg14.921
r_dihedral_angle_1_deg7.86
r_scangle_it6.053
r_scbond_it4.512
r_mcangle_it2.855
r_angle_other_deg2.027
r_mcbond_it1.998
r_angle_refined_deg1.962
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.851
r_dihedral_angle_4_deg18.167
r_dihedral_angle_3_deg14.921
r_dihedral_angle_1_deg7.86
r_scangle_it6.053
r_scbond_it4.512
r_mcangle_it2.855
r_angle_other_deg2.027
r_mcbond_it1.998
r_angle_refined_deg1.962
r_mcbond_other0.506
r_chiral_restr0.131
r_gen_planes_refined0.017
r_bond_refined_d0.016
r_gen_planes_other0.012
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7011
Nucleic Acid Atoms
Solvent Atoms495
Heterogen Atoms136

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction