4Q1C | pdb_00004q1c

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 8 {2,2'-[{4-[(2R)-4-{[(4,6-diaminopyrimidin-2-yl)sulfanyl]methyl}-5-propyl-2,3-dihydro-1,3-thiazol-2-yl]benzene-1,2-diyl}bis(oxy)]diethanol}

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	42.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.661	α = 90
b = 68.661	β = 90
c = 119.277	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	IMAGE PLATE	MAR scanner 300 mm plate		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	30	98.8	0.051	16.57		36902	36902

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	2.12	96.1		0.716	2.04		5748

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4JLN	2	25.98	34750	34750	1864	98.11	0.20714	0.20714	0.20537	0.21	0.23832	0.24	RANDOM	29.189

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]
-2.19			-2.19		4.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.512
r_dihedral_angle_4_deg	18.318
r_dihedral_angle_3_deg	17.818
r_dihedral_angle_1_deg	7.178
r_angle_other_deg	2.403
r_angle_refined_deg	1.723
r_long_range_B_refined	0.429
r_long_range_B_other	0.427
r_mcangle_it	0.385
r_mcangle_other	0.385
r_mcbond_it	0.368
r_mcbond_other	0.368
r_scangle_other	0.361
r_scbond_it	0.34
r_scbond_other	0.34
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3757
Nucleic Acid Atoms
Solvent Atoms	109
Heterogen Atoms	114

Software

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