4Q19

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 5 {5-(4-{[(4,6-DIAMINOPYRIMIDIN-2-YL)SULFANYL]METHYL}-5-PROPYL-1,3-THIAZOL-2-YL)-2-METHOXYPHENOL}

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	285	1.5 M trisodium citrate dehydrate and 25 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.535	α = 90
b = 68.535	β = 90
c = 119.793	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2013-01-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.9785	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	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	2.09	30	98.8	0.073	14.2		32496	32496

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.21	93.9		0.679	2.46		4970

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4JLN	2.09	27.44	29814	29814	1647	95.8	0.23074	0.23074	0.2289	0.26149	RANDOM	30.104

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]
5.92			5.92		-11.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.547
r_dihedral_angle_4_deg	22.179
r_dihedral_angle_3_deg	21.891
r_dihedral_angle_1_deg	7.042
r_angle_refined_deg	1.843
r_long_range_B_refined	0.476
r_mcangle_it	0.383
r_scbond_it	0.379
r_mcbond_it	0.357
r_chiral_restr	0.122
r_bond_refined_d	0.013
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3753
Nucleic Acid Atoms
Solvent Atoms	103
Heterogen Atoms	104

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling