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NHL domain of human TRIM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 10mg/mL protein in 20mM Tris pH 7.5, 150mM NaCl, 20% (v/v) glycerol and 1mM DTT was added at a 1:1 ratio to the reservoir buffer: 0.2M potassium chloride and 24% (w/v) polyethylene glycol 3350 pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.18 α = 90 b = 83.2 β = 90 c = 132.76 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS 6M 2015-11-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.872900 ESRF ID23-1
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 1.8 39.7 99.49 0.1375 0.1552 0.07005 0.99 6.72 4.5 46050 25.43
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 1.8 1.864 1.094 1.24 0.5706 0.48 1.24
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1QF7 1.8 39.7 1.35 46046 1290 99.5 0.1782 0.1771 0.1858 0.2192 0.2282 34.11
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 23.8459 f_angle_d 1.0821 f_chiral_restr 0.0849 f_bond_d 0.012 f_plane_restr 0.0068
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4212 Nucleic Acid Atoms Solvent Atoms 377 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement XDS data reduction PHASER phasing Coot model building XSCALE data scaling