2E3K

Crystal structure of the human Brd2 second bromodomain in complexed with the acetylated histone H4 peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2DVV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	PEG4000, Ammonium Acetate,, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 45.828	α = 90
b = 128.591	β = 104.7
c = 45.847	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	ADSC QUANTUM 4		2005-05-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NW12A	1.0	Photon Factory	AR-NW12A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	50	97.7	0.048		3.7	22955	22434		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	97.9		0.166		3.7

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	2DVV	2.3	20	21151	1144	98.03	0.20447	0.20096	0.26757	RANDOM	43.691

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]
1.78		1.26	-0.85		-0.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.94
r_scangle_it	3.728
r_scbond_it	2.753
r_mcangle_it	2.424
r_angle_refined_deg	1.871
r_mcbond_it	1.489
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.196

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.94
r_scangle_it	3.728
r_scbond_it	2.753
r_mcangle_it	2.424
r_angle_refined_deg	1.871
r_mcbond_it	1.489
r_symmetry_hbond_refined	0.264
r_symmetry_vdw_refined	0.259
r_nbd_refined	0.246
r_xyhbond_nbd_refined	0.196
r_chiral_restr	0.12
r_bond_refined_d	0.023
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3766
Nucleic Acid Atoms
Solvent Atoms	412
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

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.