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Crystal structure of the first bromodomain of human BRD4 in complex with MS417 inhibitor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OSS PDB ENTRY 2OSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG3350, 0.2 M lithium sulfate, 0.1 M Tris-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.843 α = 90 b = 44.659 β = 90 c = 78.237 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 ADSC QUANTUM 270 2010-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X6A 1.000 NSLS X6A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 39.12 99.7 0.055 43.7 5.8 25982 24656 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 99.3 0.335 4.8 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) 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 PDB ENTRY 2OSS 1.4 39.12 2 2 25982 24656 1326 99.27 0.13893 0.13655 0.1346 0.1831 0.1799 RANDOM 16.875
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] 1.57 -0.96 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 11.781 r_scangle_it 7.093 r_dihedral_angle_1_deg 5.347 r_scbond_it 5.223 r_mcangle_it 3.765 r_rigid_bond_restr 2.855 r_mcbond_it 2.605 r_angle_refined_deg 2.403
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 18.241 r_dihedral_angle_3_deg 11.781 r_scangle_it 7.093 r_dihedral_angle_1_deg 5.347 r_scbond_it 5.223 r_mcangle_it 3.765 r_rigid_bond_restr 2.855 r_mcbond_it 2.605 r_angle_refined_deg 2.403 r_chiral_restr 0.343 r_bond_refined_d 0.025 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1056 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms 36
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling