3HM3

The Structure and conformation of Lys-63 linked tetra-ubiquitin

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	293	0.1M Sodium acetate, 5% PEG 3000, 50 mM Zinc acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.882	α = 90
b = 105.882	β = 90
c = 105.882	γ = 90

Symmetry
Space Group	P 21 3

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		2008-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.90020	APS	14-BM-C

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	1.96	25.68	99.6	0.081	54.367	42.9		28616

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	1.96	2.01	100		0.902		43.1

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1UBQ	1.96	25.68	27141	1448	99.58	0.1882	0.18569	0.23611	RANDOM	42.133

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.892
r_dihedral_angle_4_deg	19.941
r_dihedral_angle_3_deg	16.208
r_dihedral_angle_1_deg	6.573
r_scangle_it	4.225
r_scbond_it	2.923
r_angle_refined_deg	1.885
r_mcangle_it	1.634
r_mcbond_it	1.271
r_angle_other_deg	1.008
r_symmetry_vdw_refined	0.378
r_mcbond_other	0.348
r_symmetry_vdw_other	0.291
r_nbd_refined	0.246
r_symmetry_hbond_refined	0.238
r_xyhbond_nbd_refined	0.211
r_nbd_other	0.206
r_metal_ion_refined	0.195
r_nbtor_refined	0.175
r_chiral_restr	0.128
r_xyhbond_nbd_other	0.103
r_nbtor_other	0.089
r_symmetry_metal_ion_refined	0.046
r_bond_refined_d	0.023
r_gen_planes_refined	0.009
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2404
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	6

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling