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Bromodomain-containing protein 4 (BRD4) bromodomain 1 (BD1) complexed with ZN1-99
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, HANGING DROP 8.5 277 0.2M LiSO4, 0.1M Tris-HCl pH 8.5, 16-20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.42 49.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.187 α = 90 b = 42.229 β = 90 c = 90.627 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 CCD RAYONIX MX-300 2019-06-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.2 19.49 99.6 0.051 0.056 0.021 0.999 17.3 6.9 46415
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 93.4 0.415 0.453 0.178 0.947 6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3mxf 1.2 19.49 43953 2397 99.55 0.17 0.1691 0.1728 0.1849 0.1857 RANDOM 14.24
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] 1.08 -0.3 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.055 r_dihedral_angle_4_deg 22.806 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 5.896 r_angle_refined_deg 1.831 r_angle_other_deg 1.478 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.055 r_dihedral_angle_4_deg 22.806 r_dihedral_angle_3_deg 11.961 r_dihedral_angle_1_deg 5.896 r_angle_refined_deg 1.831 r_angle_other_deg 1.478 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1065 Nucleic Acid Atoms Solvent Atoms 159 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing