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Crystal structure of B30.2 PRYSPRY domain of TRIM67
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B2S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 293.15 20% high molecular weight PEG Smears, 0.1M acetate pH 4.5
Crystal Properties Matthews coefficient Solvent content 2.06 40.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.392 α = 90 b = 135.392 β = 90 c = 35.8 γ = 90
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 2021-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99981 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 1.65 47.87 99.9 0.063 0.069 0.021 0.999 17.7 10.6 39503
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 1.65 1.69 100 0.947 1.05 0.319 0.851 2.4 10.8
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 (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 7B2S 1.65 47.87 37611 1884 99.8 0.1559 0.1548 0.167 0.1771 0.1895 RANDOM 28.266
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] -0.52 -0.52 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.287 r_dihedral_angle_4_deg 20.613 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 7.874 r_angle_refined_deg 1.505 r_angle_other_deg 1.461 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.287 r_dihedral_angle_4_deg 20.613 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 7.874 r_angle_refined_deg 1.505 r_angle_other_deg 1.461 r_chiral_restr 0.085 r_bond_refined_d 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2567 Nucleic Acid Atoms Solvent Atoms 221 Heterogen Atoms 80
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing