9FIS | pdb_00009fis

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

X-RAY DIFFRACTION

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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
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.84	α = 90
b = 70.58	β = 92.96
c = 78.59	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		2013-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

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	2.77	52.78	97.9	0.127	6.8	3.2		20568

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	2.77	2.84	98.6		0.768	1.5	3.3

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	2.77	52.78	20530	1050	97.646	0.188	0.1848	0.186	0.2433	0.2439	69.819

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]
0.374		2.204	0.629		-1.224

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.654
r_lrange_other	15.68
r_lrange_it	15.679
r_dihedral_angle_6_deg	14.718
r_dihedral_angle_2_deg	14.395
r_scangle_it	10.903
r_scangle_other	10.901
r_mcangle_it	9.067
r_mcangle_other	9.065
r_scbond_it	6.975
r_scbond_other	6.974
r_dihedral_angle_1_deg	6.965
r_mcbond_it	6.079
r_mcbond_other	6.078
r_angle_refined_deg	1.689
r_angle_other_deg	0.58
r_nbd_refined	0.221
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.183
r_nbd_other	0.164
r_xyhbond_nbd_refined	0.144
r_symmetry_xyhbond_nbd_other	0.096
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5415
Nucleic Acid Atoms
Solvent Atoms	67
Heterogen Atoms	82

Software

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