Experiment: 3N30

Crystal Structure of cubic Zn3-hUb (human ubiquitin) adduct

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	25 mg/ml milliQ water protein solution, 25% (w/v) PEG 1450, 50 mM HEPES, 200 mM Zn acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.89	α = 90
b = 104.89	β = 90
c = 104.89	γ = 90

Symmetry
Space Group	P 43 3 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 315r	mirrors	2008-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	1.282	SOLEIL	PROXIMA 1

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	3	33.169	100	0.063	0.086	40.1	19.7	4319	4319			78.3

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)
	3	3.16	100		0.508	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	PDB ENTRY 1UBQ	3	33.169	1.95	4296	4296	197	99.88	0.2376	0.2335	0.2316	0.3177	0.3218	RANDOM

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
f_dihedral_angle_d	21.343
f_angle_d	1.324
f_chiral_restr	0.072
f_bond_d	0.011
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1203
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	6

Software

Software
Software Name	Purpose
ADSC	data collection
ILMILIONE	model building
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
ILMILIONE	phasing