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BRD4-BD1 in complex with 2-{[(3S)-1-benzylpyrrolidin-3-yl]methyl}-5-methyl-7-(1-methylpyrazol-3-yl)pyrazolo[4,3-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 = 45.59 α = 90 b = 46.53 β = 90 c = 62.97 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 2021-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL45XU 1.00 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 1.01 50 99.5 0.931 10.63 15.7 70604
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 1.01 1.07 0.916
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 1.01 37.422 70533 3618 99.468 0.19 0.1885 0.1947 0.2109 0.2154 9.503
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] -0.078 -0.021 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.414 r_dihedral_angle_4_deg 21.909 r_dihedral_angle_3_deg 12.055 r_rigid_bond_restr 10.278 r_dihedral_angle_1_deg 5.646 r_angle_other_deg 2.204 r_angle_refined_deg 2.131 r_lrange_it 1.962 r_scangle_it 1.782 r_scangle_other 1.781
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.414 r_dihedral_angle_4_deg 21.909 r_dihedral_angle_3_deg 12.055 r_rigid_bond_restr 10.278 r_dihedral_angle_1_deg 5.646 r_angle_other_deg 2.204 r_angle_refined_deg 2.131 r_lrange_it 1.962 r_scangle_it 1.782 r_scangle_other 1.781 r_lrange_other 1.723 r_scbond_it 1.569 r_scbond_other 1.569 r_mcangle_other 1.379 r_mcangle_it 1.242 r_mcbond_it 1.082 r_mcbond_other 0.973 r_nbd_refined 0.238 r_nbd_other 0.237 r_symmetry_nbd_refined 0.232 r_symmetry_nbd_other 0.212 r_nbtor_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.146 r_chiral_restr 0.126 r_xyhbond_nbd_refined 0.111 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.032 r_bond_refined_d 0.019 r_gen_planes_other 0.019 r_gen_planes_refined 0.013
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1052 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing