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Crystal structure of NHL domain of TRIM71
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FQL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293.15 20% PEG3350, 10% ethylene glycol, 0.1M bis-tris-propane pH 8.5, 0.2M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.03 39.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.75 α = 90 b = 78.674 β = 100.08 c = 92.852 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 PILATUS3 6M 2021-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 0.99999 SLS X06DA
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 2.2 45.71 99.9 0.133 0.156 0.059 0.998 7.6 6.9 25069
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 2.2 2.28 99.9 0.817 0.952 0.352 0.861 2.1 7.1
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 6fql 2.2 45.71 23870 1181 99.81 0.2338 0.232 0.2716 0.2611 RANDOM 35.363
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] 1.9 -0.47 -0.22 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.53 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 9.058 r_angle_refined_deg 1.139 r_angle_other_deg 1.091 r_chiral_restr 0.042 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 r_gen_planes_other 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.53 r_dihedral_angle_4_deg 15.236 r_dihedral_angle_3_deg 14.904 r_dihedral_angle_1_deg 9.058 r_angle_refined_deg 1.139 r_angle_other_deg 1.091 r_chiral_restr 0.042 r_gen_planes_refined 0.013 r_bond_refined_d 0.009 r_gen_planes_other 0.005 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4342 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 72
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing