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Crystal structure of TRIM25 PRYSPRY covalently bound to 2-chloro-1-[4-(3-methyl-4-phenyl-phenyl)carbonyl-1,4-diazepan-1-yl]ethanone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9.5 293 0.1 M CHES, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.35 47.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.36 α = 90 b = 68.782 β = 90 c = 69.831 γ = 90
Symmetry Space Group P 21 21 21
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 2023-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.8 49 97.64 0.05966 0.06225 0.01753 1 20.98 12 20050 20.21
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 1.8 1.9 89.86 0.3006 0.3213 0.1093 0.974 2.24 7.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.8 49 1.34 19922 971 97.64 0.2227 0.2215 0.2215 0.2449 0.2449 24.01
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.9662 f_angle_d 0.8026 f_chiral_restr 0.057 f_bond_d 0.0058 f_plane_restr 0.0058
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1583 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing