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Crystal structure of the Bromo domain 2 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 7.5 277 0.2M NaF, 0.1M BTProp, 20% PEG3350, 10% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.9 57.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.837 α = 90 b = 64.678 β = 90 c = 91.827 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 2006-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97910 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 1.7 50 99.7 0.094 0.094 6.6 4.9 69322 69114
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.76 100 4.1 6853
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1X0J 1.7 50 69114 3417 99.7 0.187 0.187 0.186 0.213 0.2231 RANDOM 20.332
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] 1.38 -0.81 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 21.482 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.874 r_scangle_it 4.77 r_scbond_it 3.053 r_mcangle_it 2.032 r_angle_refined_deg 1.749 r_mcbond_it 1.159 r_angle_other_deg 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.52 r_dihedral_angle_4_deg 21.482 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.874 r_scangle_it 4.77 r_scbond_it 3.053 r_mcangle_it 2.032 r_angle_refined_deg 1.749 r_mcbond_it 1.159 r_angle_other_deg 1.01 r_mcbond_other 0.357 r_symmetry_vdw_other 0.257 r_nbd_refined 0.228 r_symmetry_hbond_refined 0.225 r_nbd_other 0.206 r_symmetry_vdw_refined 0.201 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.107 r_nbtor_other 0.092 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3573 Nucleic Acid Atoms Solvent Atoms 475 Heterogen Atoms 48
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