4NYX

Crystal Structure of the Bromodomain of human CREBBP in complex with a dihydroquinoxalinone ligand

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DAI	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	3HMH	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	2GRC	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	2OO1	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	2OSS	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	2OUO	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	3D7C	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY
experimental model	PDB	3DWY	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	0.05M CaCl2, 0.1M TRIS, 20.0% PEG 6K, 10.0% EtGly, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.047	α = 90
b = 34.358	β = 97.72
c = 90.934	γ = 90

Symmetry
Space Group	I 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	DECTRIS PILATUS 6M		2013-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.92	Diamond	I04

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.1	45.06	98.6	0.022	0.022	23.4	3.1	49969	49269			9.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.16	96.6		0.105	0.105	7	2.6	6971

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	Ensemble of PDB entries 3DAI, 3HMH, 2GRC, 2OO1, 2OSS, 2OUO, 3D7C, and 3DWY	1.1	38.29	49962	49268	2009	98.61	0.1199	0.1193	0.1348	RANDOM	15.6912

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]
-0.32		-0.1	0.56		-0.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.459
r_sphericity_free	27.51
r_dihedral_angle_4_deg	24.893
r_dihedral_angle_3_deg	11.515
r_sphericity_bonded	9.439
r_dihedral_angle_1_deg	7.334
r_rigid_bond_restr	4.145
r_mcangle_it	2.093
r_mcbond_it	1.754
r_angle_refined_deg	1.741
r_mcbond_other	1.425
r_angle_other_deg	0.885
r_chiral_restr	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	964
Nucleic Acid Atoms
Solvent Atoms	149
Heterogen Atoms	30

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction