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Crystal structure of Harmonin-homology domain 2 (HHD2) of human RTEL1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-Q9NZ71-F1 AF-Q9NZ71-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 277 20mM Tris pH7.4, 250mM NaCl, 5% Glycerol
Crystal Properties Matthews coefficient Solvent content 2.14 42.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.64 α = 90 b = 60.96 β = 95.64 c = 79.71 γ = 90
Symmetry Space Group P 1 21 1
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-F Toroidal mirror 2020-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9763 ESRF ID23-1
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 1.599 48.336 96.8 0.053 0.999 13.48 3.47 80150 -3 31.52
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 1.599 1.6 95.3 0.64 0.802 1.73
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 AF-Q9NZ71-F1 1.599 48.156 80146 2100 96.76 0.177 0.1765 0.182 0.2012 0.2114 27.133
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] 0.174 1.443 0.144 -0.592
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 13.978 r_lrange_it 7.214 r_lrange_other 6.992 r_scangle_it 5.872 r_scangle_other 5.871 r_dihedral_angle_1_deg 4.576 r_scbond_it 3.848 r_scbond_other 3.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.695 r_dihedral_angle_4_deg 19.823 r_dihedral_angle_3_deg 13.978 r_lrange_it 7.214 r_lrange_other 6.992 r_scangle_it 5.872 r_scangle_other 5.871 r_dihedral_angle_1_deg 4.576 r_scbond_it 3.848 r_scbond_other 3.847 r_mcangle_other 3.758 r_mcangle_it 3.756 r_mcbond_it 2.657 r_mcbond_other 2.649 r_angle_other_deg 2.34 r_angle_refined_deg 1.895 r_nbd_refined 0.246 r_symmetry_nbd_other 0.206 r_nbd_other 0.201 r_xyhbond_nbd_refined 0.191 r_nbtor_refined 0.185 r_symmetry_xyhbond_nbd_refined 0.161 r_symmetry_nbd_refined 0.158 r_chiral_restr 0.108 r_symmetry_xyhbond_nbd_other 0.102 r_xyhbond_nbd_other 0.076 r_symmetry_nbtor_other 0.069 r_bond_other_d 0.036 r_bond_refined_d 0.015 r_gen_planes_refined 0.007 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4388 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data scaling PDB_EXTRACT data extraction XDS data reduction PHASER phasing