9FIU | pdb_00009fiu

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
2.39	48.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.88	α = 90
b = 68.23	β = 92.22
c = 76.88	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		2014-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	3.37	52.59	96.5	0.075	12.7	2.8		10728

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	3.37	3.46			0.806	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	3.37	52.59	10727	556	96.362	0.193	0.1876	0.1873	0.2969	0.299	121.291

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]
-0.044		-0.982	-6.682		6.781

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	23.102
r_lrange_other	23.102
r_dihedral_angle_3_deg	18.819
r_mcangle_it	16.626
r_mcangle_other	16.625
r_scangle_it	16.26
r_scangle_other	16.258
r_dihedral_angle_6_deg	13.653
r_mcbond_it	10.913
r_mcbond_other	10.913
r_scbond_it	10.525
r_scbond_other	10.524
r_dihedral_angle_1_deg	7.65
r_dihedral_angle_2_deg	5.03
r_angle_refined_deg	1.454
r_angle_other_deg	0.511
r_symmetry_nbd_refined	0.352
r_nbd_other	0.237
r_nbd_refined	0.234
r_symmetry_nbd_other	0.209
r_nbtor_refined	0.187
r_ncsr_local_group_1	0.171
r_xyhbond_nbd_refined	0.165
r_symmetry_nbtor_other	0.086
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.059
r_symmetry_xyhbond_nbd_refined	0.037
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_chiral_restr_other	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5326
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	96

Software

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