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Crystal structure of human TRIM7 PRYSPRY domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6UMB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.2 M Sodium malonate dibasic monohydrate pH 7.0, 20 % PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.258 α = 90 b = 70.905 β = 90 c = 85.503 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 EIGER X 16M 2022-10-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000030 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 1.8 46.35 99.9 0.113 0.122 0.047 0.996 7.2 6.7 35213
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 1.84 99.9 0.898 0.973 0.371 0.884 6.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.8 42.79 33425 1726 99.84 0.20589 0.20419 0.2093 0.2394 0.2417 RANDOM 24.946
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] -1.99 2.44 -0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.14 r_dihedral_angle_2_deg 11.844 r_dihedral_angle_1_deg 7.598 r_long_range_B_refined 6.11 r_long_range_B_other 6.062 r_scangle_other 2.79 r_scbond_other 1.836 r_scbond_it 1.835 r_mcangle_it 1.701 r_mcangle_other 1.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.14 r_dihedral_angle_2_deg 11.844 r_dihedral_angle_1_deg 7.598 r_long_range_B_refined 6.11 r_long_range_B_other 6.062 r_scangle_other 2.79 r_scbond_other 1.836 r_scbond_it 1.835 r_mcangle_it 1.701 r_mcangle_other 1.701 r_angle_refined_deg 1.496 r_mcbond_it 1.086 r_mcbond_other 1.086 r_angle_other_deg 0.509 r_chiral_restr 0.07 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 2700 Nucleic Acid Atoms Solvent Atoms 216 Heterogen Atoms 77
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing