5LPK

Crystal structure of the bromodomain of human EP300 bound to the inhibitor XDM1

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3I3J	apo-p300 (pdb 3I3J)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	277	PEG 3350, NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.6	α = 90
b = 61.04	β = 98.31
c = 135.68	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		2013-11-23	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)	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	1.78	41.52	99.9	0.13	0.997	7	4.8		104124

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	1.78	1.81	99.8		2.986	3.447	1.682	0.168		3.9	5094

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	apo-p300 (pdb 3I3J)	2.1	41.52	60323	3107	99.89	0.1778	0.1764	0.2029	RANDOM	41.958

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]
0.75		0.96	1.08		-2.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.423
r_dihedral_angle_3_deg	17.577
r_dihedral_angle_4_deg	14.877
r_dihedral_angle_1_deg	5.04
r_mcangle_it	1.402
r_angle_refined_deg	1.301
r_mcbond_it	0.889
r_mcbond_other	0.889
r_angle_other_deg	0.783
r_chiral_restr	0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.423
r_dihedral_angle_3_deg	17.577
r_dihedral_angle_4_deg	14.877
r_dihedral_angle_1_deg	5.04
r_mcangle_it	1.402
r_angle_refined_deg	1.301
r_mcbond_it	0.889
r_mcbond_other	0.889
r_angle_other_deg	0.783
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6722
Nucleic Acid Atoms
Solvent Atoms	483
Heterogen Atoms	268

Software

Software
Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.