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Crystal Structure of the first bromodomain of human BRD4 in complex with benzo[cd]indol-2(1H)-one ligand
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, SITTING DROP 7.5 277 20% PEG3350, 0.2M NaNO3, 0.1M HEPES, 10% EtGhly, pH 7.5
Crystal Properties Matthews coefficient Solvent content 1.89 35.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.84 α = 90 b = 45.52 β = 97.23 c = 47.15 γ = 90
Symmetry Space Group P 1 21 1
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 PSI PILATUS 6M 2015-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON OTHER 0.97776
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 46.77 94.7 0.072 0.033 0.997 12.6 5.6 15753
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 95.8 0.276 0.122 0.962 4.2 5.9 788
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 1.6 46.77 14984 757 94.43 0.1679 0.1666 0.1758 0.1913 0.1984 RANDOM 16.164
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] -0.75 1 -0.57 1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.595 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_4_deg 13.072 r_dihedral_angle_1_deg 5.237 r_angle_refined_deg 1.651 r_mcangle_it 1.61 r_angle_other_deg 1.076 r_mcbond_it 1.02 r_mcbond_other 1.008 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.595 r_dihedral_angle_3_deg 13.558 r_dihedral_angle_4_deg 13.072 r_dihedral_angle_1_deg 5.237 r_angle_refined_deg 1.651 r_mcangle_it 1.61 r_angle_other_deg 1.076 r_mcbond_it 1.02 r_mcbond_other 1.008 r_chiral_restr 0.102 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1092 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 25
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction MOLREP phasing