9FIT

Structure-guided discovery of selective USP7 inhibitors with in vivo activity

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NB8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		292	23% peg 3350, 0.6 M sodium formate, 10 mM DTT

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.764	α = 90
b = 67.688	β = 90.543
c = 77.513	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	PIXEL	Bruker PHOTON II		2014-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER X8 PROTEUM	1.542

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.2	21.66	95.4	0.1689	5.91	3.81		37692

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	2.2	2.3	91		0.5394	1.55	2.17

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.7	21.66	20723	1042	96.719	0.276	0.273	0.3281	30.517

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]
-15.773		-16.247	13.202		2.571

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.83
r_dihedral_angle_6_deg	16.265
r_dihedral_angle_2_deg	10.983
r_lrange_it	9.18
r_lrange_other	9.179
r_dihedral_angle_1_deg	7.287
r_mcangle_it	5.069
r_mcangle_other	5.069
r_scangle_it	5.026
r_scangle_other	5.026
r_mcbond_it	3.094
r_mcbond_other	3.092
r_scbond_other	3.011
r_scbond_it	3.01
r_angle_refined_deg	1.88
r_angle_other_deg	0.636
r_symmetry_nbd_refined	0.485
r_nbd_other	0.406
r_nbd_refined	0.236
r_xyhbond_nbd_refined	0.236
r_symmetry_xyhbond_nbd_other	0.236
r_symmetry_nbd_other	0.219
r_ncsr_local_group_1	0.201
r_nbtor_refined	0.197
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.084
r_symmetry_xyhbond_nbd_refined	0.035
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5273
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	90

Software

Software
Software Name	Purpose
REFMAC	refinement
SAINT	data reduction
SADABS	data scaling
AMoRE	phasing