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Crystal structure of the TRIM58 PRY-SPRY domain in complex with TRIM-473
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WLI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 294 25% (w/v) PEG 3550, 0.2 M MgCl2, 0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 1.85 33.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.284 α = 90 b = 55.284 β = 90 c = 202.763 γ = 120
Symmetry Space Group P 61 2 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 EIGER2 X 16M 2018-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
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 1.3 20.01 100 0.112 0.115 0.026 0.999 12 18.6 46465
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 1.3 1.32 100 0.959 0.986 0.228 0.806 18.6
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 1.3 20.01 44022 2323 99.95 0.14054 0.13866 0.1369 0.1775 0.1751 RANDOM 16.655
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] -0.15 -0.07 -0.15 0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.023 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_3_deg 11.489 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.996 r_long_range_B_refined 3.895 r_long_range_B_other 3.732 r_rigid_bond_restr 3.721 r_scbond_it 3.143 r_scbond_other 3.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.023 r_dihedral_angle_4_deg 19.187 r_dihedral_angle_3_deg 11.489 r_dihedral_angle_1_deg 7.253 r_scangle_other 3.996 r_long_range_B_refined 3.895 r_long_range_B_other 3.732 r_rigid_bond_restr 3.721 r_scbond_it 3.143 r_scbond_other 3.142 r_mcangle_other 2.882 r_mcangle_it 2.855 r_mcbond_it 2.634 r_mcbond_other 2.512 r_angle_refined_deg 1.913 r_angle_other_deg 1.492 r_chiral_restr 0.377 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_gen_planes_other 0.003 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1428 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction Aimless data scaling PHASER phasing