8IKM | pdb_00008ikm

Trans complex of phospho parkin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GLC

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,1.0 M 8.5 Tris (base), BICINE, 25% v/v MPD; 25% PEG 1000, 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.804	α = 90
b = 83.804	β = 90
c = 105.033	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		2022-10-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.8856	ESRF	ID23-1

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	1.92	42.6	99.7	0.998	13.7	5.6		33029

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	1.92	1.97			0.724

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	6GLC	1.92	42.6	31316	1675	99.635	0.206	0.2048	0.2052	0.2325	0.2331	60.224

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]
-0.904	-0.452		-0.904		2.933

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.933
r_dihedral_angle_3_deg	17.322
r_dihedral_angle_4_deg	15.914
r_lrange_it	7.159
r_dihedral_angle_1_deg	5.698
r_mcangle_it	5.05
r_scangle_it	4.996
r_scbond_it	3.821
r_mcbond_it	3.699
r_rigid_bond_restr	0.839
r_angle_refined_deg	0.829
r_nbtor_refined	0.302
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.146
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.072
r_metal_ion_refined	0.029
r_gen_planes_refined	0.003
r_bond_refined_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2911
Nucleic Acid Atoms
Solvent Atoms	96
Heterogen Atoms	19

Software

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