8T91

Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and myo-IP6

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	12% PEG8000, 100mM HEPES pH 7.0, 10mM NaH2PO4, 10% Ethylene Glycol, 5mM ADP and 10mM MgCl2, then soaked in 25% PEG8000, 100mM HEPES pH 7.0, 20% Ethylene Glycol with 5mM myo-IP6, 5mM ADP and 10mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.517	α = 90
b = 103.569	β = 90
c = 103.427	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 EIGER X 16M		2021-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

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	2.55	50	98.8	0.099	0.106	0.036	0.985	8.9	8.1		11331

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.59	96.7		0.54	0.589	0.227	0.883		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	2.56	48.4	10547	570	96.65	0.19074	0.18817	0.23743	RANDOM	35.215

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]
			0.02		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.228
r_dihedral_angle_4_deg	25.845
r_dihedral_angle_3_deg	17.692
r_long_range_B_refined	7.832
r_long_range_B_other	7.832
r_dihedral_angle_1_deg	7.543
r_scangle_other	4.372
r_mcangle_it	3.96
r_mcangle_other	3.959
r_scbond_it	2.669
r_scbond_other	2.621
r_mcbond_it	2.35
r_mcbond_other	2.332
r_angle_refined_deg	1.505
r_angle_other_deg	1.238
r_chiral_restr	0.082
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1772
Nucleic Acid Atoms
Solvent Atoms	87
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
DENZO	data reduction
PHASER	phasing