☰ Navigation Tabs
Human TDO (hTDO) in complex with NLG919 analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6PYZ PDB entry 6PYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 293 50 mM sodium citrate, pH 5.6, 2% Tacsimate, pH 5.0, 5% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.68 54.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.263 α = 90 b = 153.811 β = 90 c = 87.975 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 2017-01-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.979 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.299 29.968 99.7 0.998 7.1 1.9 86779
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 2.3 2.34 98.9 0.999 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 6PYZ 2.3 29.95 86779 4304 99.604 0.192 0.1894 0.1892 0.2364 0.2367 50.866
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] -0.299 -1.115 1.415
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.561 r_dihedral_angle_3_deg 17.514 r_dihedral_angle_4_deg 17.34 r_lrange_other 10.841 r_lrange_it 10.837 r_scangle_it 6.692 r_scangle_other 6.692 r_mcangle_other 6.229 r_mcangle_it 6.228 r_dihedral_angle_1_deg 5.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.561 r_dihedral_angle_3_deg 17.514 r_dihedral_angle_4_deg 17.34 r_lrange_other 10.841 r_lrange_it 10.837 r_scangle_it 6.692 r_scangle_other 6.692 r_mcangle_other 6.229 r_mcangle_it 6.228 r_dihedral_angle_1_deg 5.41 r_scbond_it 4.233 r_scbond_other 4.233 r_mcbond_it 4.081 r_mcbond_other 4.072 r_angle_refined_deg 1.509 r_angle_other_deg 1.267 r_symmetry_nbd_refined 0.208 r_nbd_refined 0.207 r_nbd_other 0.193 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.165 r_xyhbond_nbd_refined 0.139 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.073 r_bond_refined_d 0.008 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 11364 Nucleic Acid Atoms Solvent Atoms 397 Heterogen Atoms 320
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing