3UV2

Crystal structure of the bromodomain of human nucleosome-remodeling factor subunit BPTF

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NXB	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OO1	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OSS	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2OUO	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	2RFJ	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI
experimental model	PDB	3DAI	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	0.10M Na/KPO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 27.141	α = 90
b = 66.809	β = 106.16
c = 39.259	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	100	IMAGE PLATE	RIGAKU RAXIS IV		2008-07-03	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	1.58	25	93.3	0.05	0.05	15.9	3.7	18460	17223			19.6

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	1.58	1.67	79.5		0.518	0.518	1.5	3.4	2102

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI	1.58	25	18457	17222	881	93.31	0.1647	0.1647	0.1623	0.209	RANDOM	18.3808

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]
0.23		0.59	-0.51		0.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.25
r_dihedral_angle_4_deg	17.842
r_dihedral_angle_3_deg	12.553
r_dihedral_angle_1_deg	4.967
r_angle_refined_deg	1.671
r_angle_other_deg	0.957
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.25
r_dihedral_angle_4_deg	17.842
r_dihedral_angle_3_deg	12.553
r_dihedral_angle_1_deg	4.967
r_angle_refined_deg	1.671
r_angle_other_deg	0.957
r_chiral_restr	0.098
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	983
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
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 R01GM133198.