4NYW | pdb_00004nyw

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	7.5	277	20% PEG 3350, 9% Ethylene Glycol, 0.18M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	49.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.966	α = 90
b = 49.917	β = 90
c = 80.16	γ = 90

Symmetry
Space Group	P 21 21 21

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 2M		2011-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9173	Diamond	I04-1

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	1.42	19.69	98.4	0.097	0.097	15.1	11.7	26900	26470			14

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	1.42	1.5	98.4		0.866	0.866	2	7.4	3748

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	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	1.43	19.69	26941	26424	1330	98.08	0.1638	0.1625	0.17	0.1867	0.2	RANDOM	17.8195

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]
0.94			0.31		-1.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.531
r_dihedral_angle_3_deg	10.77
r_dihedral_angle_4_deg	10.711
r_dihedral_angle_1_deg	5.482
r_angle_refined_deg	1.529
r_angle_other_deg	1.125
r_chiral_restr	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.005
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	968
Nucleic Acid Atoms
Solvent Atoms	186
Heterogen Atoms	39

Software

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