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Crystal structure of acetyltransferase Eis from M. tuberculosis in complex with venlafaxine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3R1K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 294 Tris-HCl pH 8.5 (0.1 M), PEG 8000 (10% w/v), and (NH4)2SO4 (0.5 M)
Crystal Properties Matthews coefficient Solvent content 3.98 69.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 175.008 α = 90 b = 175.008 β = 90 c = 124.366 γ = 120
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 16M 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID
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 2.1 50 98.8 0.07 1 2.1 7.8 42039
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 2.1 2.14 0.83
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 3R1K 2.1 43.79 39971 2068 98.44 0.16797 0.16667 0.1755 0.19335 0.2024 RANDOM 33.795
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] -1.4 -0.7 -1.4 4.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.479 r_dihedral_angle_4_deg 13.906 r_dihedral_angle_3_deg 13.289 r_long_range_B_refined 8.537 r_long_range_B_other 8.436 r_scangle_other 6.652 r_dihedral_angle_1_deg 6.586 r_scbond_it 4.529 r_scbond_other 4.528 r_mcangle_it 4.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.479 r_dihedral_angle_4_deg 13.906 r_dihedral_angle_3_deg 13.289 r_long_range_B_refined 8.537 r_long_range_B_other 8.436 r_scangle_other 6.652 r_dihedral_angle_1_deg 6.586 r_scbond_it 4.529 r_scbond_other 4.528 r_mcangle_it 4.406 r_mcangle_other 4.405 r_mcbond_it 2.967 r_mcbond_other 2.966 r_angle_other_deg 2.311 r_angle_refined_deg 1.62 r_chiral_restr 0.08 r_bond_other_d 0.035 r_bond_refined_d 0.011 r_gen_planes_other 0.011 r_gen_planes_refined 0.009 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 3028 Nucleic Acid Atoms Solvent Atoms 303 Heterogen Atoms 80
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing