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Crystal structure analysis of the N-terminal bromodomain of human BRD2 complexed with acetylated histone H4 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other BRD2-BD1 NATIVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, CO-CRYSTALLIZAATION 6.5 298 PEGMME 5K, AS, pH 6.50, VAPOR DIFFUSION, CO-CRYSTALLIZAATION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.3 47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.149 α = 90 b = 55.248 β = 94.12 c = 67.364 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 CCD ADSC 2004-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 SPring-8 BL44B2
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 2.04 50 99.5 0.057 3.6 26788 -3
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) 2.04 2.11 98.9 0.188 3.6
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT BRD2-BD1 NATIVE 2.04 20 25421 1345 99.3 0.194 0.192 0.231 RANDOM 31.48
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] 0.64 -1.52 -0.52 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.566 r_scangle_it 4.163 r_scbond_it 3.041 r_mcangle_it 1.523 r_angle_refined_deg 1.413 r_mcbond_it 0.812 r_symmetry_hbond_refined 0.292 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.151
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.566 r_scangle_it 4.163 r_scbond_it 3.041 r_mcangle_it 1.523 r_angle_refined_deg 1.413 r_mcbond_it 0.812 r_symmetry_hbond_refined 0.292 r_symmetry_vdw_refined 0.244 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.099 r_bond_refined_d 0.017 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2807 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling