9FIQ | pdb_00009fiq

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

X-RAY DIFFRACTION

---

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
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.754	α = 90
b = 70.461	β = 92.905
c = 77.946	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 PILATUS 6M		2013-01-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0723	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.86	50	96.7	0.066	0.081	0.047	8.9	2.9		18505

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.86	2.96	99		0.574	0.705	0.404	1.7	2.9

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	2.86	43.726	18491	948	96.458	0.202	0.1974	0.1983	0.2778	0.279	91.823

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]
-5.192		-2.297	0.864		4.538

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	20.466
r_lrange_other	17.966
r_lrange_it	17.965
r_dihedral_angle_6_deg	14.749
r_scangle_it	12.448
r_scangle_other	12.447
r_mcangle_other	11.576
r_mcangle_it	11.575
r_dihedral_angle_2_deg	9.478
r_scbond_it	8.229
r_scbond_other	8.228
r_mcbond_it	7.878
r_mcbond_other	7.876
r_dihedral_angle_1_deg	7.429
r_angle_refined_deg	1.652
r_angle_other_deg	0.558
r_symmetry_xyhbond_nbd_refined	0.274
r_nbd_other	0.26
r_nbd_refined	0.235
r_symmetry_nbd_other	0.212
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.185
r_symmetry_nbd_refined	0.157
r_symmetry_xyhbond_nbd_other	0.122
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.08
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	5310
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	80

Software

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