3BIY

Crystal structure of p300 histone acetyltransferase domain in complex with a bisubstrate inhibitor, Lys-CoA


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M HEPES sodium pH 7.5, 20% w/v polyethylene glycol 4,000, 10% v/v 2-Propanol , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1843.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.513α = 90
b = 61.513β = 90
c = 101.153γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDADSC QUANTUM 2102006-10-21MMAD
21x-rayMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X6A0.9786, 0.9789, 0.9287, 0.9193, 0.9253NSLSX6A
2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1,21.75099.90.04411.35.641358
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.71.761000.6585.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT1.726.6537202198094.880.183120.181580.21342RANDOM25.462
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]
0.030.03-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.413
r_dihedral_angle_4_deg17.215
r_dihedral_angle_3_deg13.36
r_dihedral_angle_1_deg5.614
r_scangle_it3.701
r_scbond_it2.418
r_angle_refined_deg1.411
r_mcangle_it1.349
r_mcbond_it0.882
r_nbtor_refined0.308
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.413
r_dihedral_angle_4_deg17.215
r_dihedral_angle_3_deg13.36
r_dihedral_angle_1_deg5.614
r_scangle_it3.701
r_scbond_it2.418
r_angle_refined_deg1.411
r_mcangle_it1.349
r_mcbond_it0.882
r_nbtor_refined0.308
r_symmetry_vdw_refined0.221
r_nbd_refined0.204
r_xyhbond_nbd_refined0.134
r_symmetry_hbond_refined0.128
r_chiral_restr0.094
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_metal_ion_refined
r_metal_ion_other
r_sphericity_bonded
r_symmetry_vdw_other
r_nbd_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_angle_other_deg
r_mcbond_other
r_nbtor_other
r_gen_planes_other
r_bond_other_d
r_rigid_bond_restr
r_sphericity_free
r_xyhbond_nbd_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2589
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms69

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
SHELXphasing