7A9G

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O1X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M DL-Malic acid, MES monohydrate, Tris (MMT)-buffer, pH 5.0 + 25% PEG1500
Crystal Properties
Matthews coefficientSolvent content
2.2645.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.865α = 90
b = 126.17β = 106.285
c = 79.031γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fdouble crystal monochromator2017-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P111.033213PETRA III, DESYP11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.948.55299.390.048580.048580.99712.41.992339
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.96899.380.36530.36530.7792.521.9

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-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2o1x1.948.5529233997199.3480.1540.15390.190422.378
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]
0.213-0.3011.789-1.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.044
r_dihedral_angle_4_deg14.097
r_dihedral_angle_3_deg13.567
r_dihedral_angle_1_deg6.328
r_lrange_it4.927
r_lrange_other4.912
r_scangle_it3.76
r_scangle_other3.76
r_scbond_it2.457
r_scbond_other2.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.044
r_dihedral_angle_4_deg14.097
r_dihedral_angle_3_deg13.567
r_dihedral_angle_1_deg6.328
r_lrange_it4.927
r_lrange_other4.912
r_scangle_it3.76
r_scangle_other3.76
r_scbond_it2.457
r_scbond_other2.456
r_mcangle_it2.371
r_mcangle_other2.371
r_angle_other_deg2.331
r_mcbond_it1.621
r_mcbond_other1.615
r_angle_refined_deg1.476
r_nbd_other0.273
r_symmetry_nbd_refined0.257
r_symmetry_nbd_other0.217
r_nbd_refined0.205
r_nbtor_refined0.155
r_symmetry_xyhbond_nbd_refined0.15
r_xyhbond_nbd_refined0.119
r_chiral_restr0.072
r_symmetry_nbtor_other0.072
r_bond_other_d0.035
r_symmetry_xyhbond_nbd_other0.031
r_gen_planes_other0.011
r_bond_refined_d0.008
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8125
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms220

Software

Software
Software NamePurpose
REFMACrefinement
pointlessdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building