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Crystal structure of B30.2 PRYSPRY domain of TRIM11
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 20% PEG3350, 10% ethylene glycol, 0.2M sodium sulfate
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.636 α = 90 b = 42.018 β = 99.44 c = 68.584 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 100 PIXEL DECTRIS EIGER2 X 16M 2020-10-25 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 1.93 43.36 99.2 0.065 0.078 0.032 0.998 12.3 5.9 27861
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 1.93 2 99.4 0.764 0.921 0.369 0.794 2 6.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2iwg 1.93 43.36 26443 1407 99.05 0.1702 0.1683 0.2049 0.2225 RANDOM 44.167
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] -0.41 -0.56 1.33 -0.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.172 r_dihedral_angle_4_deg 21.676 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 8.247 r_angle_refined_deg 1.459 r_angle_other_deg 1.251 r_chiral_restr 0.071 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.172 r_dihedral_angle_4_deg 21.676 r_dihedral_angle_3_deg 12.73 r_dihedral_angle_1_deg 8.247 r_angle_refined_deg 1.459 r_angle_other_deg 1.251 r_chiral_restr 0.071 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2829 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 59
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing