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Crystal structure of the N-terminus R100L bromodomain mutant of human BRD2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ALH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 1 M ammonium sulfate, 0.1 M MES pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.45 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.381 α = 90 b = 55.757 β = 94.76 c = 68.451 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 PILATUS 6M 2014-04-25 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) R Merge I (Observed) R Sym I (Observed) 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 1.79 29.44 99.5 0.063 0.042 14.2 5.9 40528 40528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.83 93.5 0.79 2 5.5
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 4ALH 1.79 29.44 38475 2052 99.44 0.18293 0.18081 0.1899 0.22267 0.2271 RANDOM 36.282
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] 1 -0.22 -0.59 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_4_deg 14.549 r_dihedral_angle_3_deg 13.746 r_long_range_B_refined 6.43 r_long_range_B_other 6.386 r_dihedral_angle_1_deg 5.242 r_scangle_other 4.373 r_mcangle_it 2.795 r_mcangle_other 2.794 r_scbond_it 2.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.907 r_dihedral_angle_4_deg 14.549 r_dihedral_angle_3_deg 13.746 r_long_range_B_refined 6.43 r_long_range_B_other 6.386 r_dihedral_angle_1_deg 5.242 r_scangle_other 4.373 r_mcangle_it 2.795 r_mcangle_other 2.794 r_scbond_it 2.794 r_scbond_other 2.789 r_mcbond_it 1.926 r_mcbond_other 1.926 r_angle_refined_deg 1.902 r_angle_other_deg 1.032 r_chiral_restr 0.117 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 2707 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing