4I1H

Structure of Parkin E3 ligase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I1F	PDB ENTRY 4I1F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	283	0.1 M Tris, pH 6.5, 0.2 M sodium chloride, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 383K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87.11	α = 90
b = 133.93	β = 90
c = 66.21	γ = 90

Symmetry
Space Group	C 2 2 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	RIGAKU SATURN 944+		2012-11-02	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 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	16.971	82	0.111	12.1	6.1	26566	21783

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	2.11	36.3		0.398	3.6	5.5

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	PDB ENTRY 4I1F	2	16.971	21783	1089	81.95	0.18239	0.18068	0.21537	RANDOM	20.871

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]
-0.68			0.24		0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.57
r_dihedral_angle_4_deg	16.963
r_dihedral_angle_3_deg	14.071
r_dihedral_angle_1_deg	6.75
r_angle_refined_deg	1.842
r_chiral_restr	0.118
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
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	2399
Nucleic Acid Atoms
Solvent Atoms	263
Heterogen Atoms	8

Software

Software
Software Name	Purpose
StructureStudio	data collection
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
REFMAC	phasing