4Q1E | pdb_00004q1e

Human dCK C4S-S74E mutant in complex with UDP and the inhibitor 10 {2-{[(1R/S)-1-{2-[3-(2-fluoroethoxy)-4-methoxyphenyl]-5-methyl-1,3-thiazol 4-yl}ethyl]sulfanyl}pyrimidine-4,6-diamine}

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
2.21	44.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.736	α = 90
b = 68.736	β = 90
c = 122.206	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	93	IMAGE PLATE	RIGAKU RAXIS IV++		2013-05-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.85	30	96.9	0.028	21.62		46762	46762

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	1.85	1.96	82.8		0.404	1.99		6415

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	1.85	27.92	43747	43747	2273	95.37	0.17609	0.17609	0.17399	0.18	0.21765	0.23	RANDOM	38.281

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]
-6.71			-6.71		13.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.675
r_dihedral_angle_4_deg	18.363
r_dihedral_angle_3_deg	16.7
r_dihedral_angle_1_deg	6.131
r_long_range_B_refined	5.4
r_long_range_B_other	5.352
r_scangle_other	3.54
r_mcangle_it	3.4
r_mcangle_other	3.4
r_mcbond_it	2.497
r_mcbond_other	2.491
r_scbond_it	2.473
r_scbond_other	2.473
r_angle_refined_deg	1.673
r_angle_other_deg	0.961
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3785
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	166

Software

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