8WZO | pdb_00008wzo

Parkin in complex with phospho NEDD8

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5N2W

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.976	α = 90
b = 47.747	β = 105.38
c = 127.859	γ = 90

Symmetry
Space Group	I 1 2 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 EIGER X 9M		2023-09-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.8731	ESRF	ID30B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.25	44.52	99.8	0.993	8.4	4.3		21772

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	2.25	2.32			0.643

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5N2W	2.25	40.947	21769	1097	99.689	0.209	0.2072	0.2082	0.2485	0.2517	45.106

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]
-0.35		-1.342	-0.216		1.133

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.26
r_dihedral_angle_4_deg	17.773
r_dihedral_angle_3_deg	16.868
r_lrange_it	6.373
r_dihedral_angle_1_deg	5.645
r_scangle_it	2.89
r_mcangle_it	2.858
r_scbond_it	1.774
r_mcbond_it	1.616
r_angle_refined_deg	1.026
r_nbtor_refined	0.299
r_nbd_refined	0.184
r_symmetry_nbd_refined	0.179
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.121
r_chiral_restr	0.078
r_bond_refined_d	0.004
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2929
Nucleic Acid Atoms
Solvent Atoms	174
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing