7CM2

The Crystal Structure of human USP7 USP domain from Biortus

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M Tris pH8.5, 25% PEG3,350

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.05	α = 90
b = 69.131	β = 96.076
c = 76.858	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 EIGER X 16M		2020-04-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL17U1	0.97918	SSRF	BL17U1

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	2.25	19.685	99.7	0.066	12	3.7		37704

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	2.25	2.32			0.66

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1nb8	2.25	19.685	37690	1822	99.593	0.198	0.1963	0.236	44.569

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]
-1.202		1.008	3.45		-2.408

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.744
r_dihedral_angle_4_deg	14.389
r_dihedral_angle_3_deg	14.35
r_dihedral_angle_1_deg	6.555
r_lrange_it	5.067
r_lrange_other	5.021
r_mcangle_it	3.022
r_mcangle_other	3.021
r_scangle_it	2.752
r_scangle_other	2.752
r_mcbond_it	1.736
r_mcbond_other	1.736
r_scbond_it	1.589
r_scbond_other	1.588
r_angle_refined_deg	1.177
r_angle_other_deg	1.081
r_nbd_refined	0.173
r_symmetry_nbd_other	0.165
r_nbtor_refined	0.151
r_xyhbond_nbd_refined	0.131
r_nbd_other	0.124
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.07
r_symmetry_xyhbond_nbd_refined	0.067
r_chiral_restr	0.043
r_gen_planes_refined	0.003
r_bond_refined_d	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5499
Nucleic Acid Atoms
Solvent Atoms	252
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing