7ZI5 | pdb_00007zi5

Crystal structure of dCK C4S-S74E mutant in complex with UDP and the OR0274 inhibitor

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4KCG

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	285	1 M Sodium citrate, 67 mM HEPES

Crystal Properties
Matthews coefficient	Solvent content
2.22	44.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.755	α = 90
b = 68.755	β = 90
c = 123.088	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		2020-02-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.991869	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	2	48.62	99.4	0.119	0.121	0.998	14.83	25.002		20613			59.043

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	2	2.12	96.7		1.657	1.69	0.777	1.31	25.528

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4KCG	2	48.62	19577	1031	99.57	0.1952	0.1934	0.2	0.2276	0.23	RANDOM	55.119

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]
0.21			0.21		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.667
r_dihedral_angle_3_deg	15.954
r_dihedral_angle_4_deg	13.052
r_dihedral_angle_1_deg	6.234
r_angle_refined_deg	1.575
r_angle_other_deg	1.31
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.667
r_dihedral_angle_3_deg	15.954
r_dihedral_angle_4_deg	13.052
r_dihedral_angle_1_deg	6.234
r_angle_refined_deg	1.575
r_angle_other_deg	1.31
r_chiral_restr	0.077
r_bond_refined_d	0.009
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	1919
Nucleic Acid Atoms
Solvent Atoms	46
Heterogen Atoms	60

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 R01GM157729.