☰ Navigation Tabs
TRIM21 PrySpry domain bound to an enhanced PRLX-93936 analog
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-P19474-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 4.2 M Sodium Formate; 100 mM Tris-HCl, pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.03 59.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.317 α = 90 b = 99.317 β = 90 c = 50.403 γ = 90
Symmetry Space Group P 41 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 PIXEL DECTRIS PILATUS 6M 2024-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97946 SSRL BL12-2
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 1.84 99.32 99.8 0.998 7.4 26.1 22542
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 1.9 1.93 100 0.344
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 2.1 70.326 14428 731 94.753 0.199 0.1953 0.2061 0.2647 0.2678 62.801
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] -3.012 -3.012 6.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.912 r_dihedral_angle_3_deg 16.508 r_lrange_it 13.934 r_lrange_other 13.933 r_dihedral_angle_6_deg 13.88 r_scangle_it 9.98 r_scangle_other 9.976 r_dihedral_angle_1_deg 8.491 r_mcangle_it 8.067 r_mcangle_other 8.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.912 r_dihedral_angle_3_deg 16.508 r_lrange_it 13.934 r_lrange_other 13.933 r_dihedral_angle_6_deg 13.88 r_scangle_it 9.98 r_scangle_other 9.976 r_dihedral_angle_1_deg 8.491 r_mcangle_it 8.067 r_mcangle_other 8.066 r_scbond_it 6.374 r_scbond_other 6.371 r_mcbond_it 5.449 r_mcbond_other 5.385 r_angle_refined_deg 1.507 r_angle_other_deg 0.517 r_symmetry_xyhbond_nbd_refined 0.252 r_nbd_other 0.212 r_nbd_refined 0.208 r_symmetry_nbd_other 0.206 r_nbtor_refined 0.186 r_xyhbond_nbd_refined 0.181 r_symmetry_nbd_refined 0.146 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.073 r_chiral_restr_other 0.032 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_symmetry_xyhbond_nbd_other 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1449 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing