5IID

Crystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5-hydroxy-4H-chromen-4-one

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MB4	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	3DAI	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	3HMH	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	2GRC	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	2OSS	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	2OUO	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	3D7C	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY
experimental model	PDB	3DWY	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	0.20M Na2SO4 0.1M BTProp pH 8.5 20.0% PEG 3350 10.0% EtGly

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.5	α = 90
b = 56.4	β = 90
c = 139.48	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	IMAGE PLATE	RIGAKU RAXIS IV		2011-07-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.52

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	2.4	18.632	99.3	0.104	0.104	10.4	4.6		13364

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)
1	2.4	2.53	97		0.784	1	3.5

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	Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY	2.4	18.6	12658	659	99.12	0.2207	0.2175	0.2817	RANDOM	38.291

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]
0.34			2.5		-2.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.064
r_dihedral_angle_3_deg	16.609
r_dihedral_angle_4_deg	16.185
r_dihedral_angle_1_deg	5.378
r_angle_refined_deg	1.471
r_angle_other_deg	1.167
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.064
r_dihedral_angle_3_deg	16.609
r_dihedral_angle_4_deg	16.185
r_dihedral_angle_1_deg	5.378
r_angle_refined_deg	1.471
r_angle_other_deg	1.167
r_chiral_restr	0.075
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1894
Nucleic Acid Atoms
Solvent Atoms	49
Heterogen Atoms	40

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	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.