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M. tuberculosis meets European Lead Factory: identification and structural characterization of novel Rv0183 inhibitors using X-ray crystallography: ELF8
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7P0Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 PEG 1000, PEG 3350, MPD, HEPES, MOPS, CHAPS, CHAPSO, Sodium glycocholate hydrate, Taurocholic acid sodium salt hydrate
Crystal Properties Matthews coefficient Solvent content 2.26 30.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.687 α = 90 b = 91.104 β = 90 c = 40.426 γ = 90
Symmetry Space Group P 21 21 2
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 EIGER2 X 16M 2022-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033230 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 37.65 99.85 0.01921 0.999 19.7 2 29055 19.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.864 0.959
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 37.65 1.34 29038 1454 99.87 0.1679 0.1662 0.1663 0.2016 0.2016 21.61
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 8.944 f_angle_d 0.918 f_chiral_restr 0.066 f_plane_restr 0.01 f_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2122 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms 59
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing