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Crystal structure of NHL domain of TRIM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6D69
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 25% Medium molecular weight PEG Smears, 0.1M MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.88 34.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.62 α = 74.06 b = 44.223 β = 86.93 c = 68.23 γ = 62.38
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 2020-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00003 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 1.6 38.5 91.1 0.048 0.058 0.026 0.998 15.9 4.7 52021
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 1.6 1.64 92.1 0.227 0.293 0.131 0.962 5.1 4.9
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 6d69 1.6 38.5 49455 2555 91.04 0.1576 0.1558 0.1675 0.1927 0.2027 RANDOM 22.533
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] 0.03 -0.28 0.71 -0.4 -0.32 -0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.521 r_dihedral_angle_4_deg 15.668 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 7.239 r_angle_refined_deg 1.515 r_angle_other_deg 1.425 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.521 r_dihedral_angle_4_deg 15.668 r_dihedral_angle_3_deg 12.915 r_dihedral_angle_1_deg 7.239 r_angle_refined_deg 1.515 r_angle_other_deg 1.425 r_chiral_restr 0.092 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4159 Nucleic Acid Atoms Solvent Atoms 425 Heterogen Atoms 40
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing