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The pmTcDH complex structure with an inhibitor SeCN
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8Q9X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 288 0.2M Sodium formate, 20% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.03 α = 90 b = 96.67 β = 90 c = 147.25 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 4M 2022-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.967700 ESRF MASSIF-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.8 50 96.5 0.077 0.087 0.996 12.22 4.3 86192
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 0.987 1.13 0.758
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 (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 1.8 44.14 81806 4386 96.48 0.19116 0.18877 0.1982 0.23533 0.2468 RANDOM 21.124
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] 0.27 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_rigid_bond_restr 33.152 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 7.816 r_long_range_B_refined 4.819 r_scbond_it 3.178 r_mcangle_it 2.734 r_angle_refined_deg 2.256 r_mcbond_it 2.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.561 r_rigid_bond_restr 33.152 r_dihedral_angle_4_deg 19.341 r_dihedral_angle_3_deg 12.487 r_dihedral_angle_1_deg 7.816 r_long_range_B_refined 4.819 r_scbond_it 3.178 r_mcangle_it 2.734 r_angle_refined_deg 2.256 r_mcbond_it 2.236 r_chiral_restr 0.158 r_gen_planes_refined 0.017 r_bond_refined_d 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7271 Nucleic Acid Atoms Solvent Atoms 850 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction MOLREP phasing