3NUD

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with phenylalanine


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529520MM 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 295K
Crystal Properties
Matthews coefficientSolvent content
3.9668.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 204.65α = 90
b = 204.65β = 90
c = 66.61γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray123IMAGE PLATERIGAKU RAXIS IV++OSMIC BLUE MIRRORS2005-05-24MSINGLE 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
1339.697.20.1645.62.63313633136336.2
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)
133.07797.20.34432.6831363

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 REPLACEMENTTHROUGHOUT2B7O339.5529566157496.50.215170.212270.2694RANDOM32.676
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]
0.630.320.63-0.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.469
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg14.952
r_dihedral_angle_1_deg5.488
r_scangle_it5.143
r_scbond_it3.124
r_mcangle_it2.447
r_mcbond_it1.333
r_angle_other_deg1.27
r_angle_refined_deg1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.469
r_dihedral_angle_4_deg15.204
r_dihedral_angle_3_deg14.952
r_dihedral_angle_1_deg5.488
r_scangle_it5.143
r_scbond_it3.124
r_mcangle_it2.447
r_mcbond_it1.333
r_angle_other_deg1.27
r_angle_refined_deg1.16
r_mcbond_other0.188
r_chiral_restr0.071
r_bond_refined_d0.012
r_gen_planes_refined0.011
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6756
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms85

Software

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