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Crystal Structure of the second bromodomain of BRD2 in complex with RT53
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 277 30% PEG1000
0.1M MMT pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.68 54.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.409 α = 90 b = 66.72 β = 90 c = 129.613 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2017-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim I (All) Rpim 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 1.138 29.661 99.5 0.043 0.047 0.019 16.1 5.6 101581 101581
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.2 96.9 0.435 0.435 0.511 0.264 1.8 3.5
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 3ONI 1.14 29.66 99362 2019 99.71 0.1312 0.1309 0.1407 0.143 0.1572 RANDOM 16.716
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] -0.2 0.33 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.561 r_dihedral_angle_4_deg 23.974 r_sphericity_free 20.259 r_dihedral_angle_3_deg 10.307 r_sphericity_bonded 10.05 r_dihedral_angle_1_deg 4.907 r_rigid_bond_restr 1.944 r_angle_refined_deg 1.757 r_angle_other_deg 0.994 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.561 r_dihedral_angle_4_deg 23.974 r_sphericity_free 20.259 r_dihedral_angle_3_deg 10.307 r_sphericity_bonded 10.05 r_dihedral_angle_1_deg 4.907 r_rigid_bond_restr 1.944 r_angle_refined_deg 1.757 r_angle_other_deg 0.994 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1797 Nucleic Acid Atoms Solvent Atoms 349 Heterogen Atoms 76
Software Software Software Name Purpose SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction