8T92

Crystal structure of Terrestrivirus Inositol pyrophosphatase kinase in complex with ADP and scyllo-D-(1,2,3,4)-IP4

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 D-scyllo- (1,2,3,4)IP4, 5mM ADP and 10mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.532	α = 90
b = 104.128	β = 90
c = 103.862	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		2021-12-16	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	2.3	50	99.2	0.138	0.143	0.034	0.978	8.4	19.8		15183

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	2.3	2.34	99.2		0.903	0.933	0.224	0.873		15.6

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	2.3	37.33	13443	728	91.88	0.17142	0.16832	0.22845	RANDOM	30.676

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]
0.03			-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.397
r_dihedral_angle_4_deg	27.507
r_dihedral_angle_3_deg	17.911
r_long_range_B_refined	8.979
r_long_range_B_other	8.584
r_dihedral_angle_1_deg	7.62
r_scangle_other	6.772
r_mcangle_other	4.763
r_mcangle_it	4.753
r_scbond_it	4.601
r_scbond_other	4.291
r_mcbond_it	3.023
r_mcbond_other	2.958
r_angle_refined_deg	1.851
r_angle_other_deg	1.339
r_chiral_restr	0.101
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
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	1764
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	62

Software

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