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BRD4-BD1 in complex with 7-[4-chloro-1-(tetrahydropyran-4-ylmethyl)imidazol-2-yl]-5-methyl-2-{[(2R)-2-methyl-4-methylsulfonyl-piperazin-1-yl]methyl}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 7 293 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 = 41.187 α = 90 b = 51.915 β = 90 c = 57.827 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 2020-11-25 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 50 99.5 0.967 4.88 5.74 61645
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 1.1 0.598
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.007 38.631 61602 3151 93.009 0.146 0.1447 0.1624 0.1816 7.499
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] -0.066 -0.046 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.713 r_rigid_bond_restr 15.39 r_dihedral_angle_4_deg 13.771 r_dihedral_angle_3_deg 10.256 r_dihedral_angle_1_deg 5.49 r_angle_other_deg 2.214 r_scangle_it 2.084 r_scangle_other 2.083 r_angle_refined_deg 1.991 r_lrange_it 1.989
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.713 r_rigid_bond_restr 15.39 r_dihedral_angle_4_deg 13.771 r_dihedral_angle_3_deg 10.256 r_dihedral_angle_1_deg 5.49 r_angle_other_deg 2.214 r_scangle_it 2.084 r_scangle_other 2.083 r_angle_refined_deg 1.991 r_lrange_it 1.989 r_lrange_other 1.805 r_scbond_it 1.742 r_scbond_other 1.74 r_mcangle_it 1.056 r_mcangle_other 1.056 r_mcbond_it 0.831 r_mcbond_other 0.809 r_nbd_other 0.269 r_symmetry_nbd_refined 0.239 r_nbd_refined 0.23 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.166 r_chiral_restr 0.157 r_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.073 r_bond_other_d 0.032 r_xyhbond_nbd_other 0.032 r_gen_planes_other 0.02 r_bond_refined_d 0.019 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1047 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing