☰ Navigation Tabs
Crystal structure of the human bromodomain of EP300 bound to the inhibitor XDM-CBP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NYX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 6.5 277 KSCN, NaBr, PEG 6000, PEG 8000, PEG 10000
Crystal Properties Matthews coefficient Solvent content 2.25 45.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.92 α = 90 b = 82.433 β = 110.77 c = 42.608 γ = 90
Symmetry Space Group P 1 21 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 DECTRIS EIGER X 16M 2016-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000 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 1.6 41.22 97.9 0.051 0.061 0.033 0.998 14.2 3.4 31598
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 1.6 1.63 97.9 0.419 0.496 0.263 0.8 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4NYX 1.6 41.22 30091 1483 97.76 0.1634 0.1624 0.1708 0.1854 0.1946 RANDOM 20.09
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] 0.99 0.1 -0.84 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 17.256 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.883 r_angle_refined_deg 1.353 r_angle_other_deg 0.904 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.329 r_dihedral_angle_4_deg 17.256 r_dihedral_angle_3_deg 11.802 r_dihedral_angle_1_deg 4.883 r_angle_refined_deg 1.353 r_angle_other_deg 0.904 r_chiral_restr 0.067 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1943 Nucleic Acid Atoms Solvent Atoms 362 Heterogen Atoms 74
Software Software Software Name Purpose XDS data reduction Aimless data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction