4UN2

Crystal structure of the UBA domain of Dsk2 in complex with Ubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1UBQ	PDB ENTRIES 1UBQ AND 2BWB
experimental model	PDB	2BWB	PDB ENTRIES 1UBQ AND 2BWB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.5, 20% PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
3.19	62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.971	α = 90
b = 77.972	β = 90
c = 49.485	γ = 120

Symmetry
Space Group	P 31 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	PIXEL	DECTRIS PILATUS 6M	DYNAMICALLY BENDABLE MIRROR	2011-05-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	1.52	67.5	99.5	0.05	27.78	8.07		27296		2

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	1.52	1.62	98.1		0.37	4.55	7.93

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	PDB ENTRIES 1UBQ AND 2BWB	1.51	67.52	27090	1359	99.22	0.15921	0.15722	0.16	0.19615	0.2	RANDOM	20.21

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]
-0.28	-0.14		-0.28		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.837
r_sphericity_free	30.19
r_sphericity_bonded	19.09
r_dihedral_angle_4_deg	18.616
r_dihedral_angle_3_deg	14.686
r_rigid_bond_restr	6.477
r_dihedral_angle_1_deg	5.904
r_angle_refined_deg	2.087
r_angle_other_deg	1.097
r_chiral_restr	0.16
r_bond_refined_d	0.023
r_gen_planes_refined	0.01
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	893
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms

Software

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