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Crystal structure of the second bromodomain of the human Brd2 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1X0J BRD2-BD1(PDB entry:1X0J)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 298 PEG4000, AMMONIUM ACETATE, PH 6.5, VAPOR DIFFUSION, TEMPERATURE 298K
Crystal Properties Matthews coefficient Solvent content 2.3 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.782 α = 90 b = 52.604 β = 90 c = 32.059 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 120 CCD RIGAKU JUPITER 210 2004-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 1.8 50 99.5 0.063 6.8 11743 -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) 1.8 1.86 95.2 0.238 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(PDB entry:1X0J) 1.8 20 11116 585 0.188 0.188 0.239 RANDOM 19.8
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]
RMS Deviations Key Refinement Restraint Deviation c_improper_angle_d 0.85 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot
RMS Deviations Key Refinement Restraint Deviation c_improper_angle_d 0.85 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 913 Nucleic Acid Atoms Solvent Atoms 270 Heterogen Atoms 15
Software Software Software Name Purpose MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling