9FIR | pdb_00009fir

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
2.22	44.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.94	α = 90
b = 66.78	β = 94.6
c = 76.31	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		2012-10-29	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	2.76	54.4	97	0.134	8.6	3		18158

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	2.76	2.83	99.2		0.737	2	3.2

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	2.76	54.4	18148	926	96.676	0.219	0.2138	0.214	0.3216	0.3205	61.915

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]
1.247		2.266	0.686		-2.269

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.941
r_lrange_it	18.929
r_lrange_other	18.928
r_dihedral_angle_6_deg	15.182
r_scangle_it	15.122
r_scangle_other	15.12
r_dihedral_angle_2_deg	15.058
r_mcangle_other	13.495
r_mcangle_it	13.492
r_scbond_it	10.668
r_scbond_other	10.667
r_mcbond_other	9.814
r_mcbond_it	9.813
r_dihedral_angle_1_deg	7.814
r_angle_refined_deg	2.23
r_angle_other_deg	0.739
r_nbd_refined	0.223
r_nbd_other	0.218
r_symmetry_nbd_other	0.213
r_ncsr_local_group_1	0.207
r_xyhbond_nbd_refined	0.201
r_symmetry_xyhbond_nbd_refined	0.197
r_symmetry_nbd_refined	0.193
r_nbtor_refined	0.192
r_symmetry_xyhbond_nbd_other	0.149
r_chiral_restr	0.113
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5253
Nucleic Acid Atoms
Solvent Atoms	55
Heterogen Atoms	70

Software

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