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Crystal structure of tryptophan synthase from M. tuberculosis - aminoacrylate and BRD4592-bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TCF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 289 8% tacsimate pH 8.0, 20% PEG3350, 10 mM BaCl2, 1 mM BRD4592, soaked with 100 mM CsCl and 50 mM L-Ser, cryo 16% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 3.1 60.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.092 α = 90 b = 159.875 β = 90 c = 165.331 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 CCD ADSC QUANTUM 315r mirrors 2015-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97934 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 30 99.9 0.138 12.96 6.3 138958 -3
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 2.4 2.44 99.9 0.649 1.69 5.8
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5TCF 2.4 30 136019 2712 99.5 0.18082 0.18024 0.1841 0.21074 0.2142 RANDOM 41.368
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] 0.92 1.48 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 12.61 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.108 r_long_range_B_other 3.107 r_angle_refined_deg 1.291 r_scangle_other 1.118 r_mcangle_it 0.973 r_mcangle_other 0.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 16.29 r_dihedral_angle_3_deg 12.61 r_dihedral_angle_1_deg 5.795 r_long_range_B_refined 3.108 r_long_range_B_other 3.107 r_angle_refined_deg 1.291 r_scangle_other 1.118 r_mcangle_it 0.973 r_mcangle_other 0.973 r_angle_other_deg 0.933 r_scbond_it 0.658 r_scbond_other 0.65 r_mcbond_it 0.552 r_mcbond_other 0.552 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19082 Nucleic Acid Atoms Solvent Atoms 720 Heterogen Atoms 271
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling