8FHL

Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293.15	0.2 M sodium isothiocyanate, 20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.091	α = 90
b = 86.359	β = 90
c = 211.581	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	PIXEL	DECTRIS EIGER2 X 16M		2022-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.979180	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2	41.343	99.8	0.187	0.195	0.055	0.997	10.3	13.1		29908

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	2.05			0.367

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	PDB entry 8D5F	2.194	41.343	22463	1110	99.113	0.212	0.2096	0.2479	50.643

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]
-2.124			5.423		-3.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.435
r_dihedral_angle_3_deg	14.886
r_dihedral_angle_2_deg	13.319
r_lrange_it	10.451
r_scangle_it	7.408
r_dihedral_angle_1_deg	6.992
r_scbond_it	5.18
r_mcangle_it	5.008
r_mcbond_it	3.582
r_angle_refined_deg	1.392
r_nbtor_refined	0.306
r_xyhbond_nbd_refined	0.291
r_nbd_refined	0.22
r_symmetry_xyhbond_nbd_refined	0.175
r_symmetry_nbd_refined	0.133
r_chiral_restr	0.086
r_metal_ion_refined	0.061
r_gen_planes_refined	0.009
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2822
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing