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Crystal structure analysis of the second bromodomain of BRD2 covalently linked to b-mercaptoethanol
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 22% PEG 2000, 5mM b-ME, 10% Glycerol, 50mM Tris-Cl
Crystal Properties Matthews coefficient Solvent content 2.25 45.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.19 α = 90 b = 52.45 β = 90 c = 71.87 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 2015-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.90 RRCAT INDUS-2 PX-BL21
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 1.4 42.367 98.3 0.079 0.086 0.035 0.998 12.9 6 24042
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.48 97 0.583 0.639 0.256 2.9 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 20 22848 1173 97.87 0.14501 0.14366 0.1471 0.17155 0.1698 RANDOM 16.333
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] 0.21 -0.18 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_sphericity_free 30.572 r_dihedral_angle_4_deg 22.036 r_dihedral_angle_3_deg 12.297 r_sphericity_bonded 11.081 r_dihedral_angle_1_deg 4.411 r_rigid_bond_restr 1.672 r_angle_refined_deg 1.268 r_chiral_restr 0.083 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.765 r_sphericity_free 30.572 r_dihedral_angle_4_deg 22.036 r_dihedral_angle_3_deg 12.297 r_sphericity_bonded 11.081 r_dihedral_angle_1_deg 4.411 r_rigid_bond_restr 1.672 r_angle_refined_deg 1.268 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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_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 942 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALA data scaling Coot model building PDB_EXTRACT data extraction iMOSFLM data reduction MOLREP phasing HKL data reduction