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Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 8
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, HANGING DROP 281 0.2 M calcium chloride and 20 % wt/vol PEG-3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.015 α = 90 b = 80.015 β = 90 c = 134.469 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 X 16M 2022-02-09 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 3.1 134.47 97.1 0.16 0.171 0.059 0.997 11 7.9 4853 64.5
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 3.1 3.27 1.115 1.186 0.398 0.721 2.3
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 3.1 69.3 4645 207 96.44 0.21502 0.21021 0.2483 0.33826 0.358 RANDOM 60.508
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 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_3_deg 23.018 r_dihedral_angle_4_deg 14.453 r_long_range_B_refined 13.325 r_dihedral_angle_1_deg 9.369 r_mcangle_it 7.612 r_mcbond_it 4.764 r_scbond_it 4.721 r_angle_refined_deg 1.679 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.552 r_dihedral_angle_3_deg 23.018 r_dihedral_angle_4_deg 14.453 r_long_range_B_refined 13.325 r_dihedral_angle_1_deg 9.369 r_mcangle_it 7.612 r_mcbond_it 4.764 r_scbond_it 4.721 r_angle_refined_deg 1.679 r_chiral_restr 0.121 r_gen_planes_refined 0.006 r_bond_refined_d 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1471 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing