6NFT | pdb_00006nft

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	2 M sodium/potassium phosphate pH 7.0, 1.1% DMSO (v/v), 25% ethylene glycol (v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.87	57.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.87	α = 90
b = 85.04	β = 99
c = 59.84	γ = 90

Symmetry
Space Group	C 1 2 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	CCD	RIGAKU SATURN A200		2018-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.54178

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	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	1.65	26.94	99.2	0.084	0.097	0.048	0.998	10.7	4		36423

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	97.7		0.916	1.064	0.532	0.591		3.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	1.65	26.94	34601	1821	99.06	0.1816	0.1802	0.19	0.2062	0.21	RANDOM	17.248

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]
-0.48		-0.56	0.61		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.955
r_dihedral_angle_4_deg	14.968
r_dihedral_angle_3_deg	11.427
r_dihedral_angle_1_deg	7.302
r_angle_refined_deg	1.655
r_angle_other_deg	1.502
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.955
r_dihedral_angle_4_deg	14.968
r_dihedral_angle_3_deg	11.427
r_dihedral_angle_1_deg	7.302
r_angle_refined_deg	1.655
r_angle_other_deg	1.502
r_chiral_restr	0.086
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1787
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	61

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

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 R01GM157729.