6P9G | pdb_00006p9g

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with 2-(4-oxoquinazolin-3(4H)-yl)propanoic acid

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6DXH	DIMPLE/REFMAC rigid body refinement of coordinates from PDB entry 6DXH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	291	1.75 M ammonium sulfate, 0.2 M sodium acetate, 0.1 M sodium cacodylate, 1.1% v/v dimethyl sulfoxide, 25% v/v ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.846	α = 90
b = 82.405	β = 90
c = 99.819	γ = 90

Symmetry
Space Group	I 2 2 2

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		2019-02-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.84	43.15	99.9	0.068	0.074	0.03	0.999	19.7	6.3		17416

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	1.84	1.88	99.2		1.791	1.96	0.788	0.859		6.3

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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	DIMPLE/REFMAC rigid body refinement of coordinates from PDB entry 6DXH	2.1	41	11293	586	99.86	0.2253	0.2241	0.24	0.2477	0.25	38.743

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]
-3.4			7.4		-4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.079
r_dihedral_angle_4_deg	21.092
r_dihedral_angle_3_deg	12.372
r_dihedral_angle_1_deg	7.096
r_angle_refined_deg	1.682
r_angle_other_deg	1.356
r_chiral_restr	0.069
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.079
r_dihedral_angle_4_deg	21.092
r_dihedral_angle_3_deg	12.372
r_dihedral_angle_1_deg	7.096
r_angle_refined_deg	1.682
r_angle_other_deg	1.356
r_chiral_restr	0.069
r_bond_refined_d	0.01
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	893
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	30

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
REFMAC	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 R01GM157729.