☰ Navigation Tabs
Crystal structure of NHL domain of TRIM3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7B2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 2.4M AmmSO4
Crystal Properties Matthews coefficient Solvent content 2.31 46.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.933 α = 90 b = 58.933 β = 90 c = 161.229 γ = 90
Symmetry Space Group P 41 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 2020-10-25 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 1.7 47.58 97.1 0.058 0.062 0.016 0.999 24.6 16 31138
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 1.7 1.74 94.5 0.587 0.622 0.148 0.94 3.8 17.3
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 7B2R 1.7 47.58 29599 1522 96.56 0.1839 0.1823 0.1916 0.215 0.2185 RANDOM 37.717
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] 0.45 0.45 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.025 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_1_deg 7.341 r_angle_refined_deg 1.538 r_angle_other_deg 1.405 r_chiral_restr 0.093 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 32.025 r_dihedral_angle_4_deg 16.925 r_dihedral_angle_3_deg 14.308 r_dihedral_angle_1_deg 7.341 r_angle_refined_deg 1.538 r_angle_other_deg 1.405 r_chiral_restr 0.093 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 2105 Nucleic Acid Atoms Solvent Atoms 141 Heterogen Atoms 21
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing