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Crystal structure of Bromodomain-containing protein 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other BRD2-BD2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8 293 NACL, PH 8.0, VAPOR DIFFUSION, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.891 α = 90 b = 57.779 β = 90 c = 33.588 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 ADSC QUANTUM 4 2005-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1.0 Photon Factory BL-6A
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 1.77 50 93.9 0.043 6.8 13760 -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) 1.77 1.83 99.9 0.112 6.4
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-BD2 1.8 20 12364 652 93.6 0.189 0.186 0.245 RANDOM 26.57
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] -1.92 1.7 0.22
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.234 r_scbond_it 5.772 r_dihedral_angle_1_deg 5.277 r_mcangle_it 3.889 r_mcbond_it 2.963 r_angle_refined_deg 1.235 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.156
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 7.234 r_scbond_it 5.772 r_dihedral_angle_1_deg 5.277 r_mcangle_it 3.889 r_mcbond_it 2.963 r_angle_refined_deg 1.235 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.225 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.156 r_chiral_restr 0.092 r_bond_refined_d 0.019 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 925 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 2
Software Software Software Name Purpose MOLREP phasing REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling