3IPY

X-Ray structure of Human Deoxycytidine Kinase in complex with an inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.1 M sodium acetate, 25% PEG 4000, 8% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.556	α = 90
b = 74.428	β = 90
c = 239.097	γ = 90

Symmetry
Space Group	I 21 21 21

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	NOIR-1		2004-05-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.00	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.54	119.52				20090	20090

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	1P60	2.54	119.52	20090	1071	94.46	0.2168	0.21386	0.27313	RANDOM	43.486

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]
1.5			1.22		-2.72

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.038
r_dihedral_angle_4_deg	17.436
r_dihedral_angle_3_deg	17.233
r_dihedral_angle_1_deg	5.813
r_scangle_it	1.977
r_angle_refined_deg	1.404
r_scbond_it	1.222
r_mcangle_it	1.175
r_mcbond_it	0.675
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.284
r_symmetry_hbond_refined	0.22
r_nbd_refined	0.204
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.085
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3743
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	134

Software

Software
Software Name	Purpose
REFMAC	refinement