6F5H

Crystal structure of USP7 in complex with a 4-hydroxypiperidine based inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	PEG 4000, Tris, Li2-Sulfate, pH 7.75

Crystal Properties
Matthews coefficient	Solvent content
2.37	48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.865	α = 90
b = 67.328	β = 105.06
c = 80.686	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	93	PIXEL	DECTRIS PILATUS3 2M		2015-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.16	29.95	95.9	0.11	6.4	2.4		39952

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.16	2.28	96.8		0.67	1.4	2.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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		THROUGHOUT	2.16	29.95	37973	1958	95.53	0.205	0.2021	0.2624	RANDOM	55.33

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]
2.46		0.78	-2.49		-0.35

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.846
r_dihedral_angle_3_deg	16.826
r_dihedral_angle_4_deg	14.168
r_dihedral_angle_1_deg	6.761
r_angle_refined_deg	1.37
r_angle_other_deg	0.961
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.846
r_dihedral_angle_3_deg	16.826
r_dihedral_angle_4_deg	14.168
r_dihedral_angle_1_deg	6.761
r_angle_refined_deg	1.37
r_angle_other_deg	0.961
r_chiral_restr	0.084
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5600
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	89

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	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 R01GM133198.