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Crystal structure of apo TRIM24 PHD-BRD in C121 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 2M ammonium sulfate, 0.1M HEPES (pH 7.9), 2% PEG400, 8% glycerol
Crystal Properties Matthews coefficient Solvent content 2.32 46.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.9 α = 90 b = 36.907 β = 110.044 c = 129.363 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 XE 16M 2024-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.68 44.45 95.7 0.144 1.97 6.5 43525
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.71 0.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.681 44.45 43514 2124 95.656 0.212 0.2104 0.2108 0.2402 0.2411 26.174
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] -0.031 0.051 -0.017 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.086 r_dihedral_angle_3_deg 13.326 r_lrange_it 6.398 r_dihedral_angle_1_deg 6.022 r_scangle_it 5.171 r_dihedral_angle_2_deg 4.763 r_scbond_it 3.389 r_mcangle_it 3.349 r_mcbond_it 2.327 r_angle_refined_deg 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.086 r_dihedral_angle_3_deg 13.326 r_lrange_it 6.398 r_dihedral_angle_1_deg 6.022 r_scangle_it 5.171 r_dihedral_angle_2_deg 4.763 r_scbond_it 3.389 r_mcangle_it 3.349 r_mcbond_it 2.327 r_angle_refined_deg 1.602 r_nbtor_refined 0.306 r_symmetry_nbd_refined 0.225 r_nbd_refined 0.205 r_symmetry_xyhbond_nbd_refined 0.152 r_xyhbond_nbd_refined 0.14 r_metal_ion_refined 0.128 r_ncsr_local_group_1 0.108 r_chiral_restr 0.104 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2878 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing