4ZYN

Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.105	α = 90
b = 114.105	β = 90
c = 186.399	γ = 120

Symmetry
Space Group	H 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	RIGAKU SATURN 944+		2012-11-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.54	50	95	0.128	0.131	0.047	6.2	8.1		28338

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.54	2.58	69		0.123		2.7	1040

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	4K7D	2.54	36.62	28036	1485	98.95	0.1947	0.1925	0.2353	RANDOM	66.684

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]
1.9			1.9		-3.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.781
r_dihedral_angle_3_deg	17.471
r_dihedral_angle_4_deg	16.416
r_dihedral_angle_1_deg	5.77
r_mcangle_it	3.334
r_mcbond_it	1.96
r_mcbond_other	1.96
r_angle_refined_deg	1.332
r_angle_other_deg	0.968
r_chiral_restr	0.07
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5673
Nucleic Acid Atoms
Solvent Atoms	64
Heterogen Atoms	46

Software

Software
Software Name	Purpose
REFMAC	refinement
StructureStudio	data collection
PDB_EXTRACT	data extraction
XDS	data scaling
MOLREP	phasing
XDS	data reduction