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Crystal structure of the Mycobacterium tuberculosis histidinol-phosphate aminotransferase HisC in complex with the adduct PLP-BVL3572S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4R8D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 0.1 M ammonium sulfate, 0.01 M Tris, pH 7.0, 0.075 M NaCl, 15% (w/v) PEG MME 5000, 0.05 M MES, 0.025 mM PLP, TEMPERATURE 293K, VAPOR DIFFUSION, crystals were soaked in crystallization solution supplemented with BVL3572S for 1 second and cryoprotected with 20% (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.36 47.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.603 α = 90 b = 101.59 β = 90 c = 115.53 γ = 90
Symmetry Space Group P 21 21 21
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 EIGER X 9M 2021-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.737 58.42 100 0.167 0.181 0.068 0.995 7.5 7.1 82707
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.737 1.767 100 2.445 2.668 1.087 0.343 0.8 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.74 58.42 82395 4098 99.616 0.195 0.1935 0.2035 0.2306 0.2368 29.301
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] -0.04 0.054 -0.014
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 27.691 r_dihedral_angle_6_deg 16.595 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_2_deg 12.968 r_lrange_other 8.283 r_lrange_it 8.281 r_scangle_it 7.122 r_scangle_other 7.121 r_dihedral_angle_1_deg 6.777 r_mcangle_it 5.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_other_2_deg 27.691 r_dihedral_angle_6_deg 16.595 r_dihedral_angle_3_deg 13.109 r_dihedral_angle_2_deg 12.968 r_lrange_other 8.283 r_lrange_it 8.281 r_scangle_it 7.122 r_scangle_other 7.121 r_dihedral_angle_1_deg 6.777 r_mcangle_it 5.421 r_mcangle_other 5.42 r_scbond_it 4.975 r_scbond_other 4.974 r_mcbond_it 3.904 r_mcbond_other 3.904 r_angle_refined_deg 2.199 r_angle_other_deg 0.723 r_symmetry_xyhbond_nbd_refined 0.288 r_symmetry_nbd_refined 0.266 r_nbd_other 0.229 r_nbd_refined 0.215 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.106 r_ncsr_local_group_1 0.086 r_symmetry_nbtor_other 0.085 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.014 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5496 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 95
Software Software Software Name Purpose REFMAC refinement autoPROC data processing autoPROC data reduction XDS data scaling Aimless data scaling MOLREP phasing