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Ultra high resolution crystal structure of the apo- form of second bromodomain of BRD2.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2E3K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.3 300 30% PEG MME 2000, 20% glycerol, 50mM NaCl, 50mM Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 46.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.08 α = 90 b = 52.46 β = 90 c = 71.37 γ = 90
Symmetry Space Group P 2 21 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 CCD MARMOSAIC 225 mm CCD Grazing angle 2.8 mrad 2015-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.7293 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 0.94 42.24 99.7 0.089 9.5 8 78817
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 0.94 0.99 100 2.268 1 7.9
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 2e3k 0.94 20 74948 3889 99.63 0.12921 0.12841 0.1302 0.1451 0.1365 RANDOM 13.809
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 -0.25 0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.589 r_sphericity_free 29.445 r_dihedral_angle_4_deg 22.753 r_dihedral_angle_3_deg 12.101 r_sphericity_bonded 7.949 r_dihedral_angle_1_deg 4.405 r_rigid_bond_restr 2.803 r_angle_refined_deg 1.614 r_angle_other_deg 0.888 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.589 r_sphericity_free 29.445 r_dihedral_angle_4_deg 22.753 r_dihedral_angle_3_deg 12.101 r_sphericity_bonded 7.949 r_dihedral_angle_1_deg 4.405 r_rigid_bond_restr 2.803 r_angle_refined_deg 1.614 r_angle_other_deg 0.888 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 916 Nucleic Acid Atoms Solvent Atoms 164 Heterogen Atoms 51
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction Phaser_MR phasing