5BT3

Crystal structure of EP300 bromodomain in complex with SGC-CBP30 chemical probe


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I3J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.62770.1 M tri-sodium citrate dihydrate pH 5.6, 20% iso-propanol, 20% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.346.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.431α = 90
b = 53.431β = 90
c = 77.003γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9795DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.0546.2795.90.0690.0212110.8604305560526.234
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)
11.051.1750.3744.63.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3I3J1.0546.2753225277695.810.16560.164980.178RANDOM9.313
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]
-0.03-0.02-0.030.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_4_deg17.14
r_dihedral_angle_3_deg11.256
r_dihedral_angle_1_deg5.227
r_long_range_B_refined3.345
r_long_range_B_other3.344
r_angle_refined_deg1.384
r_scangle_other1.351
r_angle_other_deg0.989
r_mcangle_other0.868
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.19
r_dihedral_angle_4_deg17.14
r_dihedral_angle_3_deg11.256
r_dihedral_angle_1_deg5.227
r_long_range_B_refined3.345
r_long_range_B_other3.344
r_angle_refined_deg1.384
r_scangle_other1.351
r_angle_other_deg0.989
r_mcangle_other0.868
r_mcangle_it0.867
r_scbond_it0.834
r_scbond_other0.833
r_mcbond_it0.528
r_mcbond_other0.515
r_chiral_restr0.08
r_bond_refined_d0.009
r_gen_planes_refined0.007
r_bond_other_d0.005
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms958
Nucleic Acid Atoms
Solvent Atoms189
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing