9FIO | pdb_00009fio

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
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.26	α = 90
b = 69.91	β = 132.308
c = 75.55	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	DECTRIS PILATUS3 6M		2012-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.92	Diamond	I04-1

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	2.46	29.2	93.9	0.043	8.99	1.81		99294

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	2.46	2.61	90.6		1.106	0.83

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.6	29.194	24986	1268	98.297	0.229	0.2237	0.2237	0.3206	0.3134	89.718

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]
-0.371		0.224	1.844		-0.708

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_other	22.441
r_lrange_it	22.44
r_dihedral_angle_3_deg	20.975
r_scangle_it	19.787
r_scangle_other	19.785
r_mcangle_other	18.117
r_mcangle_it	18.116
r_scbond_it	16.233
r_scbond_other	16.23
r_dihedral_angle_2_deg	16.225
r_mcbond_it	14.978
r_mcbond_other	14.978
r_dihedral_angle_6_deg	14.127
r_dihedral_angle_1_deg	8.083
r_angle_refined_deg	2.522
r_angle_other_deg	0.814
r_symmetry_xyhbond_nbd_refined	0.692
r_nbd_other	0.245
r_nbd_refined	0.234
r_symmetry_nbd_other	0.218
r_nbtor_refined	0.195
r_symmetry_nbd_refined	0.184
r_xyhbond_nbd_refined	0.181
r_ncsr_local_group_1	0.129
r_chiral_restr	0.121
r_symmetry_xyhbond_nbd_other	0.109
r_symmetry_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.011
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5387
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	60

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
AMoRE	phasing