Experiment: 8U2O

Crystal Structure of Cdk-related protein kinase 6 (PK6) from Plasmodium falciparum in complex with inhibitor TCMDC-123995

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q8IDW1-F1-model_v4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	291	Index G5: 25% (w/v) PEG 3350, 0.1 M Tris pH 8.5, 0.2 M Lithium sulfate monohydrate. PlfaA.01252.a.A13.PW39218 at 15.9 mg/mL. His tag cleaved with 3C protease. 2mM TCMDC-123995 added prior to crystallization. plate EWC2 well E12. Puck: PSL-1008, Cryo: 80% crystallant + 20% PEG200.

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.977	α = 90
b = 46.485	β = 100.14
c = 111.278	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 XE 9M		2023-08-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 19-ID	0.9795	NSLS-II	19-ID

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	2.15	46.49	99.9	0.105	0.116	0.047	0.997	9.1	5.9		36603

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	2.15	2.22		100	0.963	1.054	0.424	0.719		6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.15	38.65	1.34	36563	1825	99.83	0.2212	0.2181	0.2281	0.2815	0.291

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	13.399
f_angle_d	1.028
f_chiral_restr	0.055
f_plane_restr	0.011
f_bond_d	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4584
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	72

Software

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