7PA3

PARK7 with covalent inhibitor JYQ-88

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	293	0.1 M Ammonium sulfate 0.1 M Bis-Tris pH 5.5 25% (w/v) PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.743	α = 90
b = 66.743	β = 90
c = 176.785	γ = 120

Symmetry
Space Group	P 65 2 2

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 EIGER2 XE 16M		2020-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.97996	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rpim I (All)	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	1.42	58.93	100	0.033	1	17.5	32.5		44987

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.42	1.44	98.9		1.416	0.335	0.8	9.1

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6M8Z	1.42	57.802	44848	2289	99.842	0.176	0.1741	0.2138	31.274

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]
3.024	1.512		3.024		-9.811

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.481
r_dihedral_angle_4_deg	17.535
r_rigid_bond_restr	13.458
r_dihedral_angle_3_deg	13.248
r_dihedral_angle_other_3_deg	12.155
r_scangle_it	7.187
r_scangle_other	7.187
r_lrange_other	6.672
r_lrange_it	6.669
r_dihedral_angle_1_deg	6.405
r_scbond_other	5.781
r_scbond_it	5.778
r_mcangle_it	5.413
r_mcangle_other	5.412
r_mcbond_it	4.72
r_mcbond_other	4.717
r_angle_refined_deg	1.985
r_angle_other_deg	1.581
r_symmetry_nbd_refined	0.262
r_nbd_other	0.222
r_nbd_refined	0.209
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.141
r_symmetry_xyhbond_nbd_refined	0.13
r_chiral_restr	0.106
r_symmetry_nbtor_other	0.081
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1375
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	25

Software

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