7ZI8

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0602 inhibitor

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	285	0.9 M Sodium citrate, 60 mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.618	α = 90
b = 68.618	β = 90
c = 121.247	γ = 90

Symmetry
Space Group	P 41 2 2

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 9M		2020-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980112	SOLEIL	PROXIMA 2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.99	48.52	99.9	0.118	0.12	0.999	18.99	25.493		20446			58.247

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.99	2.11	99.3		3.387	3.459	0.41	0.87	24.524

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4KCG	1.99	48.52	19423	1023	99.88	0.2044	0.2014	0.2634	RANDOM	54.954

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]
-0.33			-0.33		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.123
r_dihedral_angle_4_deg	17.729
r_dihedral_angle_3_deg	16.084
r_dihedral_angle_1_deg	6.458
r_angle_refined_deg	1.533
r_angle_other_deg	1.328
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.123
r_dihedral_angle_4_deg	17.729
r_dihedral_angle_3_deg	16.084
r_dihedral_angle_1_deg	6.458
r_angle_refined_deg	1.533
r_angle_other_deg	1.328
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1915
Nucleic Acid Atoms
Solvent Atoms	32
Heterogen Atoms	65

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.