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Human TDO (hTDO) in complex with LM10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TIA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.66 53.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.428 α = 90 b = 152.919 β = 90 c = 87.588 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 CCD RAYONIX MX225HE 2017-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 2.29 52.31 97.258 0.076 6.6 6.6 85859
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.41 1.512 0.139
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 FREE R-VALUE 2.29 30.002 84922 4274 97.258 0.204 0.2023 0.2069 0.2381 0.2416 57.005
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] -0.428 -0.136 0.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.366 r_dihedral_angle_3_deg 18.416 r_dihedral_angle_4_deg 16.728 r_lrange_other 11.52 r_lrange_it 11.514 r_scangle_it 8.747 r_scangle_other 8.747 r_mcangle_other 8.459 r_mcangle_it 8.457 r_dihedral_angle_1_deg 5.803
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.366 r_dihedral_angle_3_deg 18.416 r_dihedral_angle_4_deg 16.728 r_lrange_other 11.52 r_lrange_it 11.514 r_scangle_it 8.747 r_scangle_other 8.747 r_mcangle_other 8.459 r_mcangle_it 8.457 r_dihedral_angle_1_deg 5.803 r_scbond_it 5.772 r_scbond_other 5.771 r_mcbond_it 5.659 r_mcbond_other 5.656 r_angle_refined_deg 1.76 r_angle_other_deg 1.298 r_nbd_other 0.295 r_symmetry_nbd_refined 0.249 r_nbd_refined 0.223 r_symmetry_xyhbond_nbd_refined 0.2 r_symmetry_nbd_other 0.179 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.167 r_symmetry_xyhbond_nbd_other 0.123 r_ncsr_local_group_4 0.096 r_ncsr_local_group_6 0.094 r_ncsr_local_group_3 0.093 r_ncsr_local_group_2 0.09 r_ncsr_local_group_5 0.09 r_ncsr_local_group_1 0.088 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11483 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 287
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing