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Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate
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 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.865 α = 90 b = 126.17 β = 106.285 c = 79.031 γ = 90
Symmetry Space Group P 1 21 1
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 2017-10-18 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 1.9 48.552 99.39 0.04858 0.04858 0.997 12.4 1.9 92339
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 1.9 1.968 99.38 0.3653 0.3653 0.779 2.52 1.9
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 1.9 48.552 92339 971 99.348 0.154 0.1539 0.1539 0.1904 0.1904 22.378
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 -0.301 1.789 -1.559
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_1_deg 6.328 r_lrange_it 4.927 r_lrange_other 4.912 r_scangle_it 3.76 r_scangle_other 3.76 r_scbond_it 2.457 r_scbond_other 2.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.044 r_dihedral_angle_4_deg 14.097 r_dihedral_angle_3_deg 13.567 r_dihedral_angle_1_deg 6.328 r_lrange_it 4.927 r_lrange_other 4.912 r_scangle_it 3.76 r_scangle_other 3.76 r_scbond_it 2.457 r_scbond_other 2.456 r_mcangle_it 2.371 r_mcangle_other 2.371 r_angle_other_deg 2.331 r_mcbond_it 1.621 r_mcbond_other 1.615 r_angle_refined_deg 1.476 r_nbd_other 0.273 r_symmetry_nbd_refined 0.257 r_symmetry_nbd_other 0.217 r_nbd_refined 0.205 r_nbtor_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.072 r_symmetry_nbtor_other 0.072 r_bond_other_d 0.035 r_symmetry_xyhbond_nbd_other 0.031 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8125 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 220
Software Software Software Name Purpose REFMAC refinement pointless data reduction Aimless data scaling MOLREP phasing Coot model building