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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, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.06 α = 90 b = 73.05 β = 90 c = 32.3 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 2008-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97642 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 99.9 0.043 20.37 39272 39272 -3 -3 14.483
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 1.25 100 0.381 4
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 39262 39262 1927 99.88 0.118 0.117 0.116 0.1148 0.145 0.1426 RANDOM 10.389
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] 0.59 0.85 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_sphericity_free 18.774 r_dihedral_angle_4_deg 15.468 r_dihedral_angle_3_deg 12.175 r_sphericity_bonded 8.946 r_dihedral_angle_1_deg 6.708 r_scangle_it 6.304 r_scbond_it 5.121 r_mcangle_it 3.436 r_rigid_bond_restr 3.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.973 r_sphericity_free 18.774 r_dihedral_angle_4_deg 15.468 r_dihedral_angle_3_deg 12.175 r_sphericity_bonded 8.946 r_dihedral_angle_1_deg 6.708 r_scangle_it 6.304 r_scbond_it 5.121 r_mcangle_it 3.436 r_rigid_bond_restr 3.074 r_mcbond_it 2.921 r_angle_refined_deg 2.551 r_mcbond_other 1.517 r_angle_other_deg 1.248 r_xyhbond_nbd_refined 0.368 r_nbd_refined 0.322 r_symmetry_vdw_refined 0.288 r_symmetry_hbond_refined 0.288 r_symmetry_vdw_other 0.27 r_nbd_other 0.211 r_nbtor_refined 0.206 r_chiral_restr 0.156 r_nbtor_other 0.104 r_bond_refined_d 0.031 r_gen_planes_refined 0.014 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 987 Nucleic Acid Atoms Solvent Atoms 219 Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction MOLREP phasing