3T55

Crystal structure of Mycobacterium tuberculosis Indole Glycerol Phosphate Synthase (IGPS) in complex with Phenoxymethyl Benzoic Acid (PMBA)


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 298.0
Details 0.1M Sodium acetate trihydrate, 2.0 ammonium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 45.84 α = 90
b = 53.21 β = 90
c = 87.17 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 mirrors 2009-08-03
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal. SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97711 APS 19-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
2.06 50 99.9 0.118 0.118 -- 8.2 13524 13524 0.0 0.0 18.2
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
2.06 2.14 99.7 0.425 0.425 9.2 8.5 657

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 2.06 40.57 0.0 0.0 13451 13451 677 98.48 0.1878 0.1878 0.1847 0.2495 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 2.06 2.118 -- 45 781 0.216 0.28 -- 82.93
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.0498
Anisotropic B[1][1] 0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.2
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.746
r_gen_planes_refined 0.008
r_dihedral_angle_3_deg 14.133
r_mcbond_it 0.982
r_bond_other_d 0.001
r_angle_other_deg 1.032
r_dihedral_angle_4_deg 15.328
r_dihedral_angle_1_deg 5.603
r_mcangle_it 1.689
r_scangle_it 4.41
r_chiral_restr 0.101
r_mcbond_other 0.284
r_angle_refined_deg 1.759
r_bond_refined_d 0.021
r_dihedral_angle_2_deg 35.214
r_gen_planes_other 0.001
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1838
Nucleic Acid Atoms 0
Heterogen Atoms 29
Solvent Atoms 157

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
HKL-2000 data collection
HKL-2000 data reduction
HKL-2000 data scaling