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Crystal structure of B30.2 PRYSPRY domain of TRIM16
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 6.5 293.15 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 6.5, 0.2M sodium bromide
Crystal Properties Matthews coefficient Solvent content 2.52 51.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.73 α = 90 b = 55.73 β = 90 c = 159.602 γ = 90
Symmetry Space Group P 43 21 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 2020-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 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 1.75 45.69 99.9 0.058 0.065 0.021 0.999 16.3 9 26339
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 1.75 1.81 99.9 0.992 1.123 0.366 0.915 2.3 9.1
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 6flm 1.75 45.69 25014 1246 99.79 0.1647 0.163 0.1746 0.1979 0.2051 RANDOM 38.628
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] 1.4 1.4 -2.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.414 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 12.633 r_dihedral_angle_1_deg 7.931 r_angle_refined_deg 1.448 r_angle_other_deg 1.331 r_chiral_restr 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.414 r_dihedral_angle_4_deg 15.196 r_dihedral_angle_3_deg 12.633 r_dihedral_angle_1_deg 7.931 r_angle_refined_deg 1.448 r_angle_other_deg 1.331 r_chiral_restr 0.075 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1604 Nucleic Acid Atoms Solvent Atoms 149 Heterogen Atoms 61
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing