5ENB

Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with o-Tolylthiourea (SGC - Diamond I04-1 fragment screening)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MB3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1M HEPES pH 7.5 , 0.15M magnesium chloride , 30% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.3	α = 90
b = 92.17	β = 90
c = 24.25	γ = 90

Symmetry
Space Group	P 21 21 2

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		2014-06-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.9200	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.73	22.5	99.8	0.032	0.014	0.999	25.5	6.4		14789

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.73	1.78	99.9		0.746	0.307	0.822	2.6	6.7	1045

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	3MB3	1.73	22.5	14008	741	99.6	0.213	0.2118	0.2357	RANDOM	38.632

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]
-1.37			0.23		1.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.799
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	14.465
r_dihedral_angle_1_deg	6.338
r_mcangle_it	2.675
r_mcbond_it	1.842
r_mcbond_other	1.841
r_angle_refined_deg	1.733
r_angle_other_deg	1.052
r_chiral_restr	0.106

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.799
r_dihedral_angle_4_deg	14.685
r_dihedral_angle_3_deg	14.465
r_dihedral_angle_1_deg	6.338
r_mcangle_it	2.675
r_mcbond_it	1.842
r_mcbond_other	1.841
r_angle_refined_deg	1.733
r_angle_other_deg	1.052
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	995
Nucleic Acid Atoms
Solvent Atoms	105
Heterogen Atoms	19

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	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.