9FIG | pdb_00009fig

Crystal structure of the arginine kinase Sar s 20

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		293	0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.42	49.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.476	α = 90
b = 80.904	β = 90
c = 100.504	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 EIGER2 X 16M		2020-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	0.978564	PETRA III, DESY	P11

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	1.4	48.48	99	0.066	0.079	0.042	0.999	13.8	6.5		77680

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	1.4	1.42			1.244	1.462	0.763	0.572		6.8

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.4	43.662	77614	3925	98.776	0.165	0.1639	0.1639	0.1939	0.1939	18.46

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]
-0.424			0.832		-0.408

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.765
r_dihedral_angle_3_deg	14.598
r_lrange_it	9.212
r_lrange_other	8.348
r_dihedral_angle_2_deg	8.007
r_dihedral_angle_1_deg	6.302
r_scangle_it	4.442
r_scangle_other	4.441
r_scbond_it	2.871
r_scbond_other	2.87
r_mcangle_it	2.264
r_mcangle_other	2.264
r_angle_refined_deg	1.805
r_mcbond_it	1.489
r_mcbond_other	1.489
r_angle_other_deg	0.57
r_xyhbond_nbd_refined	0.304
r_symmetry_xyhbond_nbd_refined	0.294
r_symmetry_nbd_refined	0.232
r_nbd_refined	0.23
r_nbd_other	0.21
r_symmetry_nbd_other	0.195
r_nbtor_refined	0.186
r_symmetry_xyhbond_nbd_other	0.178
r_xyhbond_nbd_other	0.14
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.08
r_bond_refined_d	0.011
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2797
Nucleic Acid Atoms
Solvent Atoms	655
Heterogen Atoms

Software

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