4S22

Crystal structure of K29 linked di-Ubiquitin

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5	285	100mM MES, 200mM potassium iodide and 25% PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 33.45	α = 90
b = 69.245	β = 90.22
c = 60.055	γ = 90

Symmetry
Space Group	P 1 21 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-F		2014-05-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1		ESRF	ID23-1

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	2.3	60.05	94.1	0.096	8.71	1.9		11542		-3	24.94

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	2.3	2.38	92.9		0.44		2

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1UBQ	2.3	60.05	22801	10922	619	94.1	0.201	0.198	0.246	RANDOM	29.16

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]
-1.47		0.19	1.3		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.248
r_dihedral_angle_4_deg	20.874
r_dihedral_angle_3_deg	15.697
r_long_range_B_refined	9.098
r_long_range_B_other	9.096
r_scangle_other	7.521
r_dihedral_angle_1_deg	6.7
r_scbond_it	5.495
r_scbond_other	5.495
r_mcangle_it	4.243
r_mcangle_other	4.241
r_mcbond_other	3.186
r_mcbond_it	3.185
r_angle_other_deg	2.078
r_angle_refined_deg	1.926
r_chiral_restr	0.114
r_bond_refined_d	0.016
r_bond_other_d	0.012
r_gen_planes_refined	0.012
r_gen_planes_other	0.01
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2366
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	16

Software

Software
Software Name	Purpose
EDNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling