9FIV | pdb_00009fiv

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	49.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.615	α = 90
b = 67.83	β = 91.256
c = 78.636	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		2014-10-17	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	2.7	21.65	99.4	0.1519	10.07	9.48		21676

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	2.7	2.8			0.6989	1.89

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	2.7	21.647	21665	1106	99.431	0.272	0.2686	0.2693	0.3304	0.3301	50.379

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		1.479	-0.73		0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	19.92
r_dihedral_angle_6_deg	14.094
r_dihedral_angle_2_deg	12.573
r_lrange_other	9.859
r_lrange_it	9.857
r_dihedral_angle_1_deg	7.598
r_mcangle_other	5.327
r_mcangle_it	5.325
r_scangle_it	5.289
r_scangle_other	5.289
r_mcbond_it	3.239
r_mcbond_other	3.239
r_scbond_it	3.129
r_scbond_other	3.128
r_angle_refined_deg	1.712
r_angle_other_deg	0.583
r_symmetry_xyhbond_nbd_refined	0.27
r_nbd_refined	0.241
r_symmetry_nbd_other	0.213
r_xyhbond_nbd_refined	0.199
r_nbtor_refined	0.193
r_nbd_other	0.188
r_symmetry_xyhbond_nbd_other	0.181
r_ncsr_local_group_1	0.147
r_symmetry_nbd_refined	0.121
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.076
r_bond_refined_d	0.007
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	5210
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	90

Software

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