3M63

Crystal structure of Ufd2 in complex with the ubiquitin-like (UBL) domain of Dsk2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.3	298	16-18% PEG 3500 200 mM Tripotassium citrate, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.03	59.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.13	α = 90
b = 125.7	β = 90
c = 181.21	γ = 90

Symmetry
Space Group	P 21 21 21

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 315r		2009-04-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.976	ESRF	ID14-4

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.4	73.501	98.6	0.062	0.062	12.9	3.8	58089	58089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.53	95.1		0.509	0.509	2.2	3.5	58089

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2QIZ	2.4	73.5	58038	58038	2951	98.26	0.21	0.21	0.206	0.27	RANDOM	42.881

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]
0.81			-0.05		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.293
r_dihedral_angle_3_deg	19.834
r_dihedral_angle_4_deg	18.844
r_dihedral_angle_1_deg	6.277
r_scangle_it	5.016
r_scbond_it	3.356
r_mcangle_it	2.113
r_angle_refined_deg	1.61
r_mcbond_it	1.13
r_chiral_restr	0.112

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.293
r_dihedral_angle_3_deg	19.834
r_dihedral_angle_4_deg	18.844
r_dihedral_angle_1_deg	6.277
r_scangle_it	5.016
r_scbond_it	3.356
r_mcangle_it	2.113
r_angle_refined_deg	1.61
r_mcbond_it	1.13
r_chiral_restr	0.112
r_bond_refined_d	0.015
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8269
Nucleic Acid Atoms
Solvent Atoms	183
Heterogen Atoms	17

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection

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 R01GM133198.