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CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRD4 IN COMPLEX with compound F5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MXF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 0.1M bis-tris-propane pH 7.9, 20% PEG3350, 0.2M sodium fluoride, 10% ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.15 42.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.235 α = 90 b = 44.141 β = 90 c = 78.441 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 PIXEL DECTRIS PILATUS3 S 6M 2018-05-04 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) 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 1.12 39.221 95.4 0.998 25.6 7 48062
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.12 1.14 0.994
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 FOURIER SYNTHESIS FREE R-VALUE 3MXF 1.12 39.221 48008 2406 95.003 0.126 0.1249 0.1242 0.1466 0.1414 11.188
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] -0.145 -0.429 0.574
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.852 r_dihedral_angle_4_deg 20.104 r_mcbond_it 10.229 r_mcbond_other 10.219 r_dihedral_angle_3_deg 10.131 r_lrange_other 9.502 r_lrange_it 9.495 r_mcangle_it 9.136 r_mcangle_other 9.129 r_scangle_it 7.959
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.852 r_dihedral_angle_4_deg 20.104 r_mcbond_it 10.229 r_mcbond_other 10.219 r_dihedral_angle_3_deg 10.131 r_lrange_other 9.502 r_lrange_it 9.495 r_mcangle_it 9.136 r_mcangle_other 9.129 r_scangle_it 7.959 r_scangle_other 7.955 r_dihedral_angle_1_deg 6.063 r_rigid_bond_restr 2.195 r_angle_refined_deg 1.726 r_angle_other_deg 1.569 r_scbond_it 1.568 r_scbond_other 1.567 r_nbd_refined 0.233 r_nbd_other 0.198 r_nbtor_refined 0.189 r_symmetry_nbd_other 0.165 r_xyhbond_nbd_refined 0.117 r_symmetry_xyhbond_nbd_refined 0.108 r_chiral_restr 0.105 r_symmetry_nbd_refined 0.094 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1053 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing