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N-TERMINAL BROMODOMAIN OF HUMAN BRD4 with GSK789
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other in house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M MES pH 6.5, 15% v/v PEG400
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.968 α = 90 b = 48.286 β = 90 c = 61.245 γ = 90
Symmetry Space Group P 21 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 RIGAKU SATURN A200 2017-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.62 37.92 91.7 0.041 17.5 2.7 15543
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 1.62 1.71 76.2 0.331 2.7 1.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE in house structure 1.624 37.919 15481 750 90.872 0.185 0.1826 0.1964 0.2246 0.235 18.456
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] 0.356 0.308 -0.664
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 20.433 r_dihedral_angle_3_deg 11.461 r_dihedral_angle_1_deg 6.07 r_lrange_it 5.433 r_lrange_other 5.431 r_scangle_it 2.973 r_scangle_other 2.971 r_mcangle_it 2.439 r_mcangle_other 2.437
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.962 r_dihedral_angle_4_deg 20.433 r_dihedral_angle_3_deg 11.461 r_dihedral_angle_1_deg 6.07 r_lrange_it 5.433 r_lrange_other 5.431 r_scangle_it 2.973 r_scangle_other 2.971 r_mcangle_it 2.439 r_mcangle_other 2.437 r_scbond_it 1.806 r_scbond_other 1.805 r_mcbond_it 1.444 r_mcbond_other 1.431 r_angle_refined_deg 1.213 r_angle_other_deg 1.212 r_nbd_refined 0.197 r_nbd_other 0.196 r_symmetry_nbd_other 0.174 r_nbtor_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.156 r_xyhbond_nbd_refined 0.14 r_symmetry_nbd_refined 0.105 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.058 r_symmetry_xyhbond_nbd_other 0.022 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1061 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling