5ENF

Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with fragment-4 N10142 (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 , 32% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.808	α = 90
b = 91.958	β = 90
c = 24.091	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		2014-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92001	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	1.37	21.76	95.4	0.057	0.032	0.991	11.9	3.6		27767

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	1.37	1.43	91.4		0.524	0.303	0.649	2.2	3.6	2973

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	1.37	21.76	26322	1409	94.42	0.181	0.1789	0.2203	RANDOM	27.512

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]
3.31			-2.35		-0.96

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	69.631
r_dihedral_angle_2_deg	28.378
r_sphericity_bonded	26.675
r_dihedral_angle_4_deg	12.637
r_dihedral_angle_3_deg	12.36
r_dihedral_angle_1_deg	5.184
r_mcangle_it	2.981
r_rigid_bond_restr	2.726
r_mcbond_it	2.621
r_mcbond_other	2.62

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	69.631
r_dihedral_angle_2_deg	28.378
r_sphericity_bonded	26.675
r_dihedral_angle_4_deg	12.637
r_dihedral_angle_3_deg	12.36
r_dihedral_angle_1_deg	5.184
r_mcangle_it	2.981
r_rigid_bond_restr	2.726
r_mcbond_it	2.621
r_mcbond_other	2.62
r_angle_refined_deg	1.724
r_angle_other_deg	1.102
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	996
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	20

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.