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Human TRIM21 PRYSPRY domain in complex with BMS-214662
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9QBA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 4.3 M Sodium Chloride
0.1 M Hepes pH 8
Crystal Properties Matthews coefficient Solvent content 4.05 69.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.142 α = 90 b = 100.142 β = 90 c = 57.489 γ = 120
Symmetry Space Group P 31 2 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 EIGER2 XE 16M 2025-03-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95374 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.1 57.49 98.8 0.059 0.061 0.014 0.996 25.1 19.7 19488
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 2.696 2.763 0.604 0.861 20.9
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 (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 2.1 50.12 18510 959 98.8 0.1976 0.19739 0.2076 0.20152 0.2121 RANDOM 63.606
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] 1.53 0.76 1.53 -4.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.998 r_long_range_B_refined 8.487 r_long_range_B_other 8.485 r_dihedral_angle_1_deg 8.363 r_scangle_other 6.669 r_mcangle_it 5.907 r_mcangle_other 5.905 r_dihedral_angle_2_deg 5.392 r_scbond_it 5.021 r_scbond_other 5.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.998 r_long_range_B_refined 8.487 r_long_range_B_other 8.485 r_dihedral_angle_1_deg 8.363 r_scangle_other 6.669 r_mcangle_it 5.907 r_mcangle_other 5.905 r_dihedral_angle_2_deg 5.392 r_scbond_it 5.021 r_scbond_other 5.02 r_mcbond_it 4.529 r_mcbond_other 4.522 r_angle_refined_deg 1.491 r_angle_other_deg 0.496 r_chiral_restr 0.068 r_gen_planes_refined 0.007 r_bond_refined_d 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1420 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 42
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PDB_EXTRACT data extraction MOLREP phasing