4RXX

Crystal Structure of the N-terminal Domain of Human Ubiquitin Specific Protease 38

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	291	Protein sample was first mixed Hampton Research Additive Screen H03 40% in 10:1 (V/V) Protein:1,3-propanediol ratio, then set up with 15% PEG8000, 0.2 M MgCl2, 0.1 M HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 291K, VAPOR DIFFUSION, HANGING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.985	α = 90
b = 102.039	β = 90
c = 135.281	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	ADSC QUANTUM 315r		2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97932	APS	19-ID

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	2.06	50	99.8	0.127	22.9	9.7		37072			29.4

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	2.06	2.1	97.3		0.82		5.9	1797

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.06	50	35715	1137	99.84	0.1906	0.1891	0.2419	RANDOM	35.898

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]
2.33			-0.6		-1.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.569
r_dihedral_angle_4_deg	22.308
r_dihedral_angle_3_deg	13.15
r_dihedral_angle_1_deg	4.487
r_mcangle_it	2.686
r_mcbond_it	1.904
r_mcbond_other	1.902
r_angle_refined_deg	1.324
r_angle_other_deg	0.783
r_chiral_restr	0.081

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.569
r_dihedral_angle_4_deg	22.308
r_dihedral_angle_3_deg	13.15
r_dihedral_angle_1_deg	4.487
r_mcangle_it	2.686
r_mcbond_it	1.904
r_mcbond_other	1.902
r_angle_refined_deg	1.324
r_angle_other_deg	0.783
r_chiral_restr	0.081
r_bond_refined_d	0.01
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	3375
Nucleic Acid Atoms
Solvent Atoms	221
Heterogen Atoms	10

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing
RESOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.