3B0F

Crystal structure of the UBA domain of p62 and its interaction with ubiquitin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	100mM Citrate buffer pH5.0, 1.8M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.967	α = 90
b = 72.967	β = 90
c = 32.56	γ = 90

Symmetry
Space Group	P 43 21 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	ADSC QUANTUM 315		2008-01-25	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315		2008-01-25	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	1.000	Photon Factory	BL-5A
2	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-5A	0.97928, 0.97909, 0.96405, 0.98317	Photon Factory	BL-5A

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	1.4	51.57	97	0.048	13.1	13.1	17371	17371

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	1.4	1.45	82.5		0.356		11

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.4	50	17323	16435	888	96.93	0.17167	0.17167	0.17011	0.20054	RANDOM	11.036

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]
-0.8			-0.8		1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.195
r_dihedral_angle_3_deg	14.544
r_dihedral_angle_4_deg	13.295
r_sphericity_free	6.591
r_dihedral_angle_1_deg	4.326
r_scangle_it	4.179
r_sphericity_bonded	3.052
r_scbond_it	3.027
r_mcangle_it	2.024
r_rigid_bond_restr	1.7
r_angle_refined_deg	1.697
r_mcbond_it	1.418
r_chiral_restr	0.116
r_bond_refined_d	0.016
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	678
Nucleic Acid Atoms
Solvent Atoms	77
Heterogen Atoms	5

Software

Software
Software Name	Purpose
SERGUI	data collection
SOLVE	phasing
REFMAC	refinement
HKL-2000	data scaling