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TRIM7 PRYSPRY in complex with a MNV1-NS3 peptide HDDFGLQ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8A5L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291.15 1 M DL-Malic Acid pH 5, 0.1 M BIS-TRIS Propane pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.3 46.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.252 α = 90 b = 53.668 β = 105.55 c = 73.595 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 80 PIXEL DECTRIS EIGER2 XE 16M 2022-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 2.37 70.91 97.4 1 6.8 3.3 15418
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 2.37 2.43 0.6
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 FREE R-VALUE 8A5L 2.37 28.337 15418 712 97.33 0.192 0.1885 0.1913 0.2637 0.2657 28.428
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] 0.572 -2.211 -0.828 1.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.592 r_dihedral_angle_4_deg 21.409 r_dihedral_angle_3_deg 17.204 r_dihedral_angle_1_deg 8.867 r_lrange_it 5.952 r_lrange_other 5.952 r_scangle_it 4.407 r_scangle_other 4.407 r_mcangle_it 3.428 r_mcangle_other 3.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.592 r_dihedral_angle_4_deg 21.409 r_dihedral_angle_3_deg 17.204 r_dihedral_angle_1_deg 8.867 r_lrange_it 5.952 r_lrange_other 5.952 r_scangle_it 4.407 r_scangle_other 4.407 r_mcangle_it 3.428 r_mcangle_other 3.427 r_scbond_it 2.855 r_scbond_other 2.855 r_mcbond_it 2.225 r_mcbond_other 2.224 r_angle_refined_deg 1.653 r_angle_other_deg 1.242 r_nbd_refined 0.193 r_symmetry_nbd_other 0.188 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.154 r_nbd_other 0.146 r_symmetry_xyhbond_nbd_refined 0.134 r_symmetry_nbd_refined 0.113 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2813 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing