8IKT | pdb_00008ikt

Ternary trans-complex of phospho-parkin with cis ACT and pUb

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8IKM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		291	0.3 M Sodium nitrate, 0.3 Sodium phosphate dibasic, 0.3 M Ammonium sulfate, Imidazole, MES monohydrate (acid), 25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.764	α = 90
b = 82.764	β = 90
c = 103.494	γ = 120

Symmetry
Space Group	P 32 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 PILATUS 6M		2023-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM07	0.9795	ESRF	BM07

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.6	38.42	99.9	0.144	0.998	17.1	13.1		13050

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	2.6	2.72			0.791

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	8IKM	2.6	38.42	12333	691	99.87	0.214	0.2125	0.2088	0.2358	0.2341	63.575

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]
-1.814	-0.907		-1.814		5.883

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.857
r_dihedral_angle_3_deg	14.863
r_dihedral_angle_4_deg	9.993
r_dihedral_angle_1_deg	5.887
r_lrange_it	5.687
r_mcangle_it	2.945
r_scangle_it	2.729
r_scbond_it	1.841
r_mcbond_it	1.836
r_angle_refined_deg	0.844
r_nbtor_refined	0.303
r_rigid_bond_restr	0.237
r_nbd_refined	0.198
r_symmetry_nbd_refined	0.188
r_symmetry_xyhbond_nbd_refined	0.159
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.063
r_bond_refined_d	0.005
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2977
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	30

Software

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