6DXT | pdb_00006dxt

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 3-(5-phenyl-1,3,4-oxadiazol-2-yl)propanoate

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2G43	pdbid 2G43

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	291	1.5 M ammonium sulfate, 0.1 M bis-tris pH 7.0, 25% ethylene glycol (v/v), 1.1% DMSO (v/v)

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.09	α = 90
b = 85.44	β = 100.29
c = 59.74	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		2018-05-23	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	1.95	30.05	95.2	0.038	0.044	0.022	0.999	16.2	3.8		20938

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	1.95	2	92.9		0.218	0.253	0.128	0.967		3.9

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdbid 2G43	1.95	30.07	19928	1010	95	0.1962	0.194	0.2	0.2419	0.25	RANDOM	25.318

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]
-0.91		-0.06	1.27		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.673
r_dihedral_angle_4_deg	14.455
r_dihedral_angle_3_deg	12.134
r_dihedral_angle_1_deg	7.173
r_angle_refined_deg	1.495
r_angle_other_deg	0.984
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.673
r_dihedral_angle_4_deg	14.455
r_dihedral_angle_3_deg	12.134
r_dihedral_angle_1_deg	7.173
r_angle_refined_deg	1.495
r_angle_other_deg	0.984
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1731
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
xia2	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.