☰ Navigation Tabs
BRD4-BD1 in complex with 5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}-7-(1-methylpyrazol-3-yl)furo[3,2-c]pyridin-4-one
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6CZU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 32.32 α = 90 b = 47.02 β = 90 c = 80.16 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 6M 2021-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.0 SPring-8 BL45XU
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 1.04 50 99.4 0.98 5.43 8.36 59251
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 1.04 1.1 0.558
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.04 40.558 59176 3052 99.405 0.177 0.175 0.1782 0.2084 0.2096 15.414
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] -0.774 0.705 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.753 r_dihedral_angle_4_deg 16.083 r_rigid_bond_restr 13.963 r_dihedral_angle_3_deg 11.556 r_dihedral_angle_1_deg 5.486 r_lrange_it 3.145 r_scangle_it 3.126 r_scangle_other 3.125 r_lrange_other 3.092 r_scbond_other 2.819
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.753 r_dihedral_angle_4_deg 16.083 r_rigid_bond_restr 13.963 r_dihedral_angle_3_deg 11.556 r_dihedral_angle_1_deg 5.486 r_lrange_it 3.145 r_scangle_it 3.126 r_scangle_other 3.125 r_lrange_other 3.092 r_scbond_other 2.819 r_scbond_it 2.815 r_angle_other_deg 2.26 r_mcangle_other 2.256 r_mcangle_it 2.249 r_angle_refined_deg 2.126 r_mcbond_other 1.799 r_mcbond_it 1.794 r_nbd_refined 0.218 r_nbd_other 0.205 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.141 r_chiral_restr 0.123 r_xyhbond_nbd_refined 0.118 r_symmetry_nbd_refined 0.089 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.031 r_gen_planes_other 0.018 r_bond_refined_d 0.017 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1043 Nucleic Acid Atoms Solvent Atoms 121 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing