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BRD4-BD1 in complex with N-cyclohexyl-1-methyl-6-{[5-methyl-7-(1-methylpyrazol-3-yl)-4-oxo-pyrazolo[4,3-c]pyridin-2-yl]methyl}azepan-1-ium-4-carboxamide 2,2,2-trifluoroacetate
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 7 293 0.1M Hepes pH 7.0, 5% MgCl2, 20% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.12 42.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.05 α = 90 b = 49.35 β = 90 c = 61.06 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 2022-02-04 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 1.18 50 100 0.998 10.94 14.7 43571
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 1.18 1.25 0.524
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 1.18 38.381 43508 2220 99.943 0.158 0.1567 0.1655 0.1856 0.1883 21.222
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] 0.799 -0.578 -0.221
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.447 r_dihedral_angle_4_deg 12.131 r_rigid_bond_restr 11.915 r_dihedral_angle_3_deg 11.539 r_dihedral_angle_1_deg 5.484 r_lrange_it 3.871 r_lrange_other 3.863 r_scangle_it 3.747 r_scangle_other 3.698 r_scbond_it 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.447 r_dihedral_angle_4_deg 12.131 r_rigid_bond_restr 11.915 r_dihedral_angle_3_deg 11.539 r_dihedral_angle_1_deg 5.484 r_lrange_it 3.871 r_lrange_other 3.863 r_scangle_it 3.747 r_scangle_other 3.698 r_scbond_it 3.26 r_scbond_other 3.242 r_mcbond_other 2.54 r_mcbond_it 2.537 r_mcangle_it 2.489 r_mcangle_other 2.487 r_angle_other_deg 2.186 r_angle_refined_deg 1.906 r_symmetry_nbd_refined 0.347 r_nbd_other 0.28 r_nbd_refined 0.275 r_symmetry_nbd_other 0.231 r_nbtor_refined 0.187 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.151 r_symmetry_xyhbond_nbd_other 0.141 r_chiral_restr 0.121 r_symmetry_nbtor_other 0.078 r_bond_other_d 0.031 r_gen_planes_other 0.02 r_bond_refined_d 0.015 r_gen_planes_refined 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 118 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing