23VK | pdb_000023vk

Crystal structure of full-length of APS kinase from Entamoeba histolytica

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	10 mM Tris-HCl (pH 8.0) 100 mM NaCl 1 mM TCEP 5 mM APS 5 mM AMP-PNP 5 mM MgCl2 0.24 M K2SO4 16% PEG3400

Crystal Properties
Matthews coefficient	Solvent content
2.91	57.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 144.449	α = 90
b = 158.387	β = 90
c = 226.163	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		2023-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.90000	SPring-8	BL44XU

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	2.59	50	99.5	0.066	0.999	14.36	6.1		79795

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	2.59	2.75			0.531	0.8

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	SAD	FREE R-VALUE	2.595	19.97	79596	3995	99.308	0.228	0.2265	0.2302	0.2648	0.2658	111.398

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]
			-0.001		0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.224
r_lrange_other	15.981
r_lrange_it	15.98
r_dihedral_angle_6_deg	13.515
r_scangle_it	11.812
r_scangle_other	11.798
r_dihedral_angle_2_deg	11.572
r_mcangle_it	11.337
r_mcangle_other	11.336
r_scbond_it	7.562
r_scbond_other	7.55
r_mcbond_it	7.388
r_mcbond_other	7.387
r_dihedral_angle_1_deg	5.899
r_angle_refined_deg	1.285
r_angle_other_deg	0.769
r_nbd_other	0.237
r_nbd_refined	0.221
r_symmetry_nbd_other	0.214
r_nbtor_refined	0.175
r_xyhbond_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbd_refined	0.114
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.07
r_gen_planes_refined	0.005
r_gen_planes_other	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14065
Nucleic Acid Atoms
Solvent Atoms	13
Heterogen Atoms	20

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
CRANK2	phasing
BUCCANEER	model building