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Crystal structure of TRIM33 alpha PHD-Bromo domain in complex with 10
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 2.43 49.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.953 α = 90 b = 79.953 β = 90 c = 134.945 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 3.2 134.95 99.5 0.066 0.077 0.037 0.999 11.2 3.8 4598 100.3
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 3.2 3.37 99.8 0.545 0.625 0.294 0.766 2.3 4.1
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 3.2 61.68 4307 256 99.28 0.23895 0.23189 0.2581 0.34854 0.3529 RANDOM 86.868
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] -0.06 -0.03 -0.06 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.127 r_dihedral_angle_4_deg 24.73 r_dihedral_angle_3_deg 23.238 r_long_range_B_refined 16.445 r_mcangle_it 9.898 r_dihedral_angle_1_deg 8.181 r_scbond_it 7.386 r_mcbond_it 6.391 r_angle_refined_deg 1.413 r_chiral_restr 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.127 r_dihedral_angle_4_deg 24.73 r_dihedral_angle_3_deg 23.238 r_long_range_B_refined 16.445 r_mcangle_it 9.898 r_dihedral_angle_1_deg 8.181 r_scbond_it 7.386 r_mcbond_it 6.391 r_angle_refined_deg 1.413 r_chiral_restr 0.11 r_bond_refined_d 0.005 r_gen_planes_refined 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 1384 Nucleic Acid Atoms Solvent Atoms 5 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction SCALA data scaling MOLREP phasing