9FHN | pdb_00009fhn

Crystal structure of the arginine kinase Der p 20.0101

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 Lithium sulfate monohydrate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.28	α = 90
b = 99.02	β = 108.056
c = 77.883	γ = 90

Symmetry
Space Group	P 1 21 1

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	Bruker PHOTON III		2022-05-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	LIQUID ANODE	Excillum MetalJet D2+ 70 kV	1.34138

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.9	59.3	90.8	0.144	0.978	4.3	2.9		49720

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94			0.5	0.708

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	1.9	59.3	40075	2044	73.106	0.272	0.2697	0.2695	0.3098	0.3098	7.484

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]
0.213		-0.444	1.494		-1.169

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.146
r_dihedral_angle_3_deg	14.45
r_dihedral_angle_2_deg	6.974
r_dihedral_angle_1_deg	6.679
r_angle_refined_deg	1.232
r_lrange_it	1.087
r_lrange_other	1.059
r_scangle_it	0.592
r_scangle_other	0.592
r_mcangle_it	0.586
r_mcangle_other	0.586
r_angle_other_deg	0.425
r_mcbond_it	0.409
r_mcbond_other	0.409
r_scbond_it	0.394
r_scbond_other	0.394
r_symmetry_xyhbond_nbd_refined	0.35
r_nbd_other	0.244
r_xyhbond_nbd_refined	0.243
r_symmetry_nbd_refined	0.221
r_nbd_refined	0.22
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.176
r_symmetry_xyhbond_nbd_other	0.151
r_ncsr_local_group_1	0.088
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.058
r_bond_refined_d	0.005
r_gen_planes_refined	0.005
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5580
Nucleic Acid Atoms
Solvent Atoms	199
Heterogen Atoms

Software

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