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Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3U5M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 281 0.2 M calcium chloride and 20 % wt/vol PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.84 56.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.965 α = 90 b = 79.965 β = 90 c = 135.497 γ = 120
Symmetry Space Group P 65 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 EIGER2 XE 16M 2022-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 3.05 135.5 100 0.182 0.189 0.051 0.995 10 13.6 5355 69
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) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.05 3.21 100 1.079 1.118 0.29 0.827 2.2 14.7
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 3U5M 3.05 69.25 5062 256 99.98 0.23379 0.22865 0.2694 0.33422 0.3565 RANDOM 69.252
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] -0.04 -0.02 -0.04 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.304 r_dihedral_angle_3_deg 21.325 r_dihedral_angle_4_deg 19.558 r_long_range_B_refined 13.902 r_long_range_B_other 13.898 r_mcangle_it 9.39 r_mcangle_other 9.385 r_scangle_other 9.045 r_dihedral_angle_1_deg 8.845 r_mcbond_other 6.106
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.304 r_dihedral_angle_3_deg 21.325 r_dihedral_angle_4_deg 19.558 r_long_range_B_refined 13.902 r_long_range_B_other 13.898 r_mcangle_it 9.39 r_mcangle_other 9.385 r_scangle_other 9.045 r_dihedral_angle_1_deg 8.845 r_mcbond_other 6.106 r_mcbond_it 6.105 r_scbond_it 5.799 r_scbond_other 5.795 r_angle_refined_deg 1.771 r_angle_other_deg 1.206 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 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 1425 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing