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Crystal structure of human TATDN1 bound to dAMP and two zinc ions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XIO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 19% PEG 8000, 100 mM HEPES pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.44 49.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.88 α = 90 b = 76.51 β = 90 c = 77.36 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 9M 2021-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.127230 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 45.3 99.36 0.06 0.999 15.93 6.62 52962 21.38
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.505 1.6 92.7 0.743 0.84 3.02 6.7
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 (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 2XIO 1.5 45.3 50313 2648 99.37 0.164 0.1627 0.1626 0.1888 0.1887 RANDOM 23.162
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] 0.1 -0.28 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_4_deg 8.49 r_dihedral_angle_1_deg 5.037 r_angle_other_deg 2.254 r_angle_refined_deg 1.542 r_chiral_restr 0.086 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.488 r_dihedral_angle_3_deg 12.579 r_dihedral_angle_4_deg 8.49 r_dihedral_angle_1_deg 5.037 r_angle_other_deg 2.254 r_angle_refined_deg 1.542 r_chiral_restr 0.086 r_bond_other_d 0.034 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2333 Nucleic Acid Atoms Solvent Atoms 417 Heterogen Atoms 56
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MoRDa phasing