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Crystal structure of the human TRIM25 coiled-coil and PRYSPRY domains
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4LTB Separate coiled-coil (PDB:4LTB) and PRYSPRY (PDB:6FLM) domains experimental model PDB 6FLM Separate coiled-coil (PDB:4LTB) and PRYSPRY (PDB:6FLM) domains
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein at 10 mg/ml was mixed in 2:1 ratio with mother liquor containing 0.2 M sodium formate, 14% PEG 3350 and 0.1 M bis-Tris pH 6.5.
Crystal Properties Matthews coefficient Solvent content 2.4 48.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.92 α = 90 b = 89.92 β = 90 c = 827.09 γ = 120
Symmetry Space Group P 61 2 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 PILATUS 6M-F 2016-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.072 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 3.6 137.85 99.5 0.136 0.151 0.999 8.18 5.36 24552
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.6 3.69 98.5 2.38 2.64 0.569 5.51
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 Separate coiled-coil (PDB:4LTB) and PRYSPRY (PDB:6FLM) domains 3.6 137.85 23260 1255 99.37 0.28877 0.28717 0.2892 0.31844 0.3132 RANDOM 219.61
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] 8.14 4.07 8.14 -26.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.093 r_long_range_B_refined 20.943 r_long_range_B_other 20.942 r_mcangle_it 15.179 r_mcangle_other 15.178 r_dihedral_angle_3_deg 14.898 r_scangle_other 12.467 r_dihedral_angle_4_deg 12.342 r_mcbond_it 9.112 r_mcbond_other 9.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.093 r_long_range_B_refined 20.943 r_long_range_B_other 20.942 r_mcangle_it 15.179 r_mcangle_other 15.178 r_dihedral_angle_3_deg 14.898 r_scangle_other 12.467 r_dihedral_angle_4_deg 12.342 r_mcbond_it 9.112 r_mcbond_other 9.111 r_scbond_it 7.016 r_scbond_other 7.015 r_dihedral_angle_1_deg 6.092 r_angle_refined_deg 1.051 r_angle_other_deg 0.854 r_chiral_restr 0.06 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8861 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing