7A9H

Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis


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
2.3247.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.987α = 108.956
b = 76.1β = 106.53
c = 79.148γ = 107.594
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-Fdouble crystal monochromator2017-12-03MSINGLE 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
11.84943.832910.02330.02330.99920.991.893268
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)
11.851.91662.530.08520.08520.9796.541.7

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-VALUE2o1x1.84943.83293268210190.850.1510.15070.173619.252
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]
-0.0440.233-0.220.6780.079-0.432
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.325
r_dihedral_angle_4_deg14.616
r_dihedral_angle_3_deg13.088
r_dihedral_angle_1_deg6.254
r_lrange_it4.36
r_lrange_other4.36
r_scangle_it2.864
r_scangle_other2.863
r_angle_other_deg2.358
r_mcangle_it2.039
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.325
r_dihedral_angle_4_deg14.616
r_dihedral_angle_3_deg13.088
r_dihedral_angle_1_deg6.254
r_lrange_it4.36
r_lrange_other4.36
r_scangle_it2.864
r_scangle_other2.863
r_angle_other_deg2.358
r_mcangle_it2.039
r_mcangle_other2.038
r_scbond_other1.805
r_scbond_it1.804
r_angle_refined_deg1.37
r_mcbond_it1.318
r_mcbond_other1.314
r_nbd_other0.223
r_symmetry_nbd_other0.213
r_nbd_refined0.205
r_symmetry_xyhbond_nbd_refined0.169
r_nbtor_refined0.152
r_symmetry_nbd_refined0.147
r_xyhbond_nbd_refined0.122
r_symmetry_xyhbond_nbd_other0.085
r_chiral_restr0.068
r_symmetry_nbtor_other0.063
r_bond_other_d0.035
r_gen_planes_other0.009
r_bond_refined_d0.007
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8162
Nucleic Acid Atoms
Solvent Atoms666
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building