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Crystal structure of bromodomain 2 of mouse Brd4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OUO PDB ENTRY 2OUO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.1M Tris/HCl, 25% PEG 2000 MME, soaked with 10 mM H3-K(ac)14 octapeptide GGK(ac)APRKQ, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.1 α = 90 b = 73.15 β = 90 c = 32.16 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 225 mm CCD 2008-05-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97886 SLS X10SA
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 1.2 19.53 95.2 0.066 23.39 37336 37336 -3 -3 15.484
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) 1.2 1.25 96.3 0.577 6.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2OUO 1.2 19.53 37326 37326 1846 95.17 0.118 0.117 0.116 0.1158 0.151 0.152 RANDOM 10.513
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 0.12 -1.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 23.395 r_sphericity_free 16.08 r_dihedral_angle_3_deg 10.514 r_sphericity_bonded 7.222 r_scangle_it 6.186 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.091 r_mcangle_it 3.587 r_mcbond_it 2.994
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.71 r_dihedral_angle_4_deg 23.395 r_sphericity_free 16.08 r_dihedral_angle_3_deg 10.514 r_sphericity_bonded 7.222 r_scangle_it 6.186 r_dihedral_angle_1_deg 6.082 r_scbond_it 5.091 r_mcangle_it 3.587 r_mcbond_it 2.994 r_rigid_bond_restr 2.908 r_angle_refined_deg 2.366 r_mcbond_other 1.423 r_angle_other_deg 1.245 r_symmetry_vdw_other 0.38 r_xyhbond_nbd_refined 0.323 r_nbd_refined 0.32 r_symmetry_vdw_refined 0.285 r_symmetry_hbond_refined 0.247 r_nbd_other 0.202 r_nbtor_refined 0.2 r_chiral_restr 0.152 r_nbtor_other 0.104 r_bond_refined_d 0.034 r_gen_planes_refined 0.015 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 950 Nucleic Acid Atoms Solvent Atoms 223 Heterogen Atoms 20
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction MOLREP phasing