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Crystal structure of human Bromodomain containing protein 3 (BRD3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0J pdb entry 1X0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 277 0.20M KSCN, 0.1M BTPop, 20% PEG3350, 10% EtGly, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.504 α = 90 b = 61.84 β = 90 c = 84.523 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 MARMOSAIC 225 mm CCD 2006-10-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 50 100 0.084 0.084 10.2 6.1 54074 54074
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.45 100 0.398 0.398 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 (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 1X0J 1.4 49.94 54073 51261 2748 99.88 0.16848 0.16761 0.1752 0.18479 0.1735 RANDOM 17.171
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] 0.86 -0.29 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.037 r_dihedral_angle_4_deg 12.234 r_dihedral_angle_3_deg 11.448 r_dihedral_angle_1_deg 4.921 r_scangle_it 2.489 r_angle_other_deg 2.091 r_scbond_it 1.668 r_angle_refined_deg 1.256 r_mcangle_it 0.962 r_mcbond_it 0.543
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.037 r_dihedral_angle_4_deg 12.234 r_dihedral_angle_3_deg 11.448 r_dihedral_angle_1_deg 4.921 r_scangle_it 2.489 r_angle_other_deg 2.091 r_scbond_it 1.668 r_angle_refined_deg 1.256 r_mcangle_it 0.962 r_mcbond_it 0.543 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.222 r_symmetry_vdw_other 0.199 r_nbtor_refined 0.195 r_nbd_other 0.174 r_symmetry_hbond_refined 0.171 r_mcbond_other 0.159 r_xyhbond_nbd_refined 0.144 r_nbtor_other 0.09 r_chiral_restr 0.071 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1899 Nucleic Acid Atoms Solvent Atoms 277 Heterogen Atoms 29
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling