9FHO | pdb_00009fho

Crystal structure of the arginine kinase Der p 20_like (putative isoform)

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	0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol monomethyl ether 550

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.561	α = 90
b = 61.894	β = 96.442
c = 61.769	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	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	1.8	48.25	97.9	0.086	0.119	0.081	0.988	6.4	3.2		33156

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	1.8	1.84			0.427	0.582	0.393	0.857		3.3

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	1.8	48.25	33139	1594	97.923	0.187	0.1847	0.1847	0.2252	0.2252	37.66

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]
-1.851		-1.743	3.346		-1.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.594
r_dihedral_angle_2_deg	15.805
r_dihedral_angle_3_deg	15.16
r_lrange_it	7.609
r_lrange_other	7.573
r_dihedral_angle_1_deg	6.645
r_scangle_it	4.186
r_scangle_other	4.185
r_mcangle_other	2.911
r_mcangle_it	2.91
r_scbond_it	2.705
r_scbond_other	2.703
r_mcbond_it	1.93
r_mcbond_other	1.929
r_angle_refined_deg	1.451
r_angle_other_deg	0.48
r_symmetry_nbd_refined	0.381
r_symmetry_xyhbond_nbd_refined	0.337
r_symmetry_xyhbond_nbd_other	0.249
r_xyhbond_nbd_refined	0.238
r_nbd_refined	0.224
r_nbd_other	0.211
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.176
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.068
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2779
Nucleic Acid Atoms
Solvent Atoms	306
Heterogen Atoms	5

Software

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