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Human DTX4 RING-DTC domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6Y5P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Morpheus Fusion A4. 0.1M Carboxylic Acids ,0.12M Alcohol ,0.1 M Buffer System 1 pH6.5 ,37.5 % Precipitant Mix 4
Crystal Properties Matthews coefficient Solvent content 3.6 66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 109.092 α = 90 b = 109.092 β = 90 c = 222.015 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS PILATUS 6M 2024-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97628 Diamond I03
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 2.8 29.13 99.9 0.997 10 28.4 20026
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 2.8 2.95 0.48 0.8
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 2.8 29.13 19963 975 99.83 0.23 0.2263 0.228 0.2936 0.2922 77.005
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] 1.395 0.698 1.395 -4.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.635 r_dihedral_angle_6_deg 13.993 r_lrange_it 8.749 r_lrange_other 8.748 r_dihedral_angle_1_deg 7.808 r_dihedral_angle_2_deg 6.769 r_mcangle_other 5.297 r_mcangle_it 5.295 r_scangle_it 5.278 r_scangle_other 5.277
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.635 r_dihedral_angle_6_deg 13.993 r_lrange_it 8.749 r_lrange_other 8.748 r_dihedral_angle_1_deg 7.808 r_dihedral_angle_2_deg 6.769 r_mcangle_other 5.297 r_mcangle_it 5.295 r_scangle_it 5.278 r_scangle_other 5.277 r_scbond_it 3.321 r_scbond_other 3.321 r_mcbond_it 3.258 r_mcbond_other 3.24 r_angle_refined_deg 1.646 r_angle_other_deg 0.573 r_nbd_refined 0.231 r_symmetry_nbd_other 0.211 r_nbd_other 0.211 r_symmetry_metal_ion_refined 0.196 r_nbtor_refined 0.186 r_symmetry_nbd_refined 0.186 r_metal_ion_refined 0.182 r_dihedral_angle_other_2_deg 0.167 r_symmetry_xyhbond_nbd_refined 0.132 r_xyhbond_nbd_refined 0.129 r_ncsr_local_group_1 0.103 r_symmetry_nbtor_other 0.085 r_chiral_restr 0.076 r_symmetry_xyhbond_nbd_other 0.065 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3474 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing