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Crystal structure of the human bromodomain of CREBBP bound to the inhibitor XDM4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DWY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 277 LiSO4, PEG 3350, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.25 45.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.03 α = 90 b = 34.13 β = 92.65 c = 40.29 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 PIXEL PSI PILATUS 6M 2015-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 44.97 89.9 0.066 0.084 0.051 0.989 10.2 2.4 12221
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 91.9 0.138 0.177 0.108 0.924 2.3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3DWY 1.7 44.97 11516 704 89.43 0.2218 0.2193 0.228 0.2599 0.2618 RANDOM 17.886
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] -0.54 0.2 1.9 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.758 r_dihedral_angle_3_deg 13.717 r_dihedral_angle_4_deg 11.565 r_dihedral_angle_1_deg 4.593 r_angle_refined_deg 1.514 r_angle_other_deg 0.976 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.758 r_dihedral_angle_3_deg 13.717 r_dihedral_angle_4_deg 11.565 r_dihedral_angle_1_deg 4.593 r_angle_refined_deg 1.514 r_angle_other_deg 0.976 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 966 Nucleic Acid Atoms Solvent Atoms 170 Heterogen Atoms 41
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction