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Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O1X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M DL-Malic acid, MES monohydrate, Tris (MMT)-buffer, pH 5.0 + 25% PEG1500
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.987 α = 108.956 b = 76.1 β = 106.53 c = 79.148 γ = 107.594
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F double crystal monochromator 2017-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033213 PETRA III, DESY P11
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.849 43.832 91 0.0233 0.0233 0.999 20.99 1.8 93268
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) Redundancy Number Unique Reflections (All) 1 1.85 1.916 62.53 0.0852 0.0852 0.979 6.54 1.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2o1x 1.849 43.832 93268 2101 90.85 0.151 0.1507 0.1507 0.1736 0.1735 19.252
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] -0.044 0.233 -0.22 0.678 0.079 -0.432
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.325 r_dihedral_angle_4_deg 14.616 r_dihedral_angle_3_deg 13.088 r_dihedral_angle_1_deg 6.254 r_lrange_it 4.36 r_lrange_other 4.36 r_scangle_it 2.864 r_scangle_other 2.863 r_angle_other_deg 2.358 r_mcangle_it 2.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.325 r_dihedral_angle_4_deg 14.616 r_dihedral_angle_3_deg 13.088 r_dihedral_angle_1_deg 6.254 r_lrange_it 4.36 r_lrange_other 4.36 r_scangle_it 2.864 r_scangle_other 2.863 r_angle_other_deg 2.358 r_mcangle_it 2.039 r_mcangle_other 2.038 r_scbond_other 1.805 r_scbond_it 1.804 r_angle_refined_deg 1.37 r_mcbond_it 1.318 r_mcbond_other 1.314 r_nbd_other 0.223 r_symmetry_nbd_other 0.213 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.169 r_nbtor_refined 0.152 r_symmetry_nbd_refined 0.147 r_xyhbond_nbd_refined 0.122 r_symmetry_xyhbond_nbd_other 0.085 r_chiral_restr 0.068 r_symmetry_nbtor_other 0.063 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8162 Nucleic Acid Atoms Solvent Atoms 666 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing Coot model building