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Crystal Structure of the First Bromodomain of Human Brd2 with the inhibitor GW841819X
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E6I PDB ENTRY 1E6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 17.5% PEG 3350, 0.2 M (NH4)2SO4, 0.1 M BIS TRIS PH 5.5.
Crystal Properties Matthews coefficient Solvent content 2.07 42.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.372 α = 90 b = 56.013 β = 93.98 c = 67.425 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 1996-06-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF ESRF
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 1.9 67.26 98.8 0.09 11.5 3.9 34166 2 23
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 1.9 2 94.6 0.44 3.3 3.5
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MIR THROUGHOUT PDB ENTRY 1E6I 1.9 67.27 32436 1730 100 0.20247 0.19995 0.24959 0.2843 RANDOM 37.229
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] 0.67 -0.04 -0.51 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.276 r_dihedral_angle_4_deg 21.436 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 4.4 r_scangle_it 2.592 r_scbond_it 1.621 r_mcangle_it 1.279 r_angle_refined_deg 1.101 r_angle_other_deg 0.795 r_mcbond_it 0.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.276 r_dihedral_angle_4_deg 21.436 r_dihedral_angle_3_deg 12.643 r_dihedral_angle_1_deg 4.4 r_scangle_it 2.592 r_scbond_it 1.621 r_mcangle_it 1.279 r_angle_refined_deg 1.101 r_angle_other_deg 0.795 r_mcbond_it 0.666 r_mcbond_other 0.102 r_chiral_restr 0.052 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2666 Nucleic Acid Atoms Solvent Atoms 306 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing