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TRIM21 PRYSPRY bound to compound 209
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.6 291.15 20% (w/v) PEG-8000, 0.1M CHES pH 9.5 (final pH 9.6)
Crystal Properties Matthews coefficient Solvent content 1.95 37.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.068 α = 90 b = 60.827 β = 112.543 c = 42.223 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 2023-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.619 Diamond I24
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 2.33 30.432 99.6 0.955 5.4 3.5 7445
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 2.33 2.41 0.296
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 2.331 30.432 7432 363 99.478 0.227 0.2224 0.234 0.3137 0.324 35.966
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] -1.762 1.354 0.154 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.979 r_dihedral_angle_3_deg 20.192 r_dihedral_angle_4_deg 14.656 r_dihedral_angle_1_deg 8.968 r_lrange_other 6.929 r_lrange_it 6.927 r_mcangle_it 4.023 r_mcangle_other 4.021 r_scangle_it 3.965 r_scangle_other 3.964
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.979 r_dihedral_angle_3_deg 20.192 r_dihedral_angle_4_deg 14.656 r_dihedral_angle_1_deg 8.968 r_lrange_other 6.929 r_lrange_it 6.927 r_mcangle_it 4.023 r_mcangle_other 4.021 r_scangle_it 3.965 r_scangle_other 3.964 r_mcbond_it 2.41 r_mcbond_other 2.402 r_scbond_it 2.397 r_scbond_other 2.396 r_angle_refined_deg 1.444 r_angle_other_deg 1.144 r_nbd_other 0.238 r_nbd_refined 0.224 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.179 r_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.082 r_symmetry_nbtor_other 0.079 r_symmetry_xyhbond_nbd_refined 0.079 r_chiral_restr 0.053 r_symmetry_xyhbond_nbd_other 0.013 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1475 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing