7EWS

Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7EGZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	0.1M Hepes-NaOH, pH 7.0, 20% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.109	α = 90
b = 77.727	β = 90
c = 162.197	γ = 90

Symmetry
Space Group	P 21 21 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		2021-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00	SPring-8	BL41XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	44.42	99.7	0.33	9	11.8		58371

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	2.03	2.17			0.74

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	7EGZ	2	44.42	57655	3039	99.97	0.19874	0.19667	0.23685	RANDOM	9.958

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]
2.71			-1.55		-1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.39
r_dihedral_angle_4_deg	18.39
r_dihedral_angle_3_deg	14.586
r_dihedral_angle_1_deg	6.161
r_long_range_B_refined	4.126
r_long_range_B_other	3.973
r_scangle_other	2.671
r_mcangle_it	1.957
r_mcangle_other	1.957
r_scbond_it	1.68
r_scbond_other	1.68
r_angle_refined_deg	1.508
r_angle_other_deg	1.38
r_mcbond_it	1.192
r_mcbond_other	1.188
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	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	6012
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms

Software

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