9FIP | pdb_00009fip

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
2.42	49.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.05	α = 90
b = 68.28	β = 92
c = 77.66	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		2012-10-10	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	3.06	77.61	96.9	0.108	7.6	2.8		14565

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	3.06	3.14	98.8		0.619		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	3.06	77.61	14514	731	96.586	0.174	0.1694	0.1693	0.2639	0.2679	91.285

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]
-4.248		-3.557	-1.747		6.229

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.295
r_lrange_it	18.052
r_lrange_other	18.052
r_dihedral_angle_6_deg	14.112
r_scangle_it	13.054
r_scangle_other	13.053
r_mcangle_it	11.229
r_mcangle_other	11.227
r_dihedral_angle_2_deg	9.272
r_scbond_it	8.369
r_scbond_other	8.368
r_mcbond_it	7.483
r_mcbond_other	7.467
r_dihedral_angle_1_deg	7.279
r_angle_refined_deg	1.525
r_angle_other_deg	0.53
r_symmetry_xyhbond_nbd_refined	0.379
r_xyhbond_nbd_other	0.237
r_nbd_refined	0.223
r_ncsr_local_group_1	0.223
r_symmetry_nbd_other	0.215
r_symmetry_nbd_refined	0.197
r_nbd_other	0.194
r_nbtor_refined	0.188
r_xyhbond_nbd_refined	0.164
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.074
r_symmetry_xyhbond_nbd_other	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5410
Nucleic Acid Atoms
Solvent Atoms	14
Heterogen Atoms	66

Software

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