3HP1

Crystal structure of human dCK R104M/D133A in complex with L-dT and ADP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1P5Z	PDB entry 1P5Z

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	295	1 microliter of protein-nucleoside-nucleotide mix and 1 microliter reservoir solution containing 0.9-1.5 M Trisodium citrate dihydrate and 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.78	α = 90
b = 79.78	β = 90
c = 93.7	γ = 90

Symmetry
Space Group	P 43 21 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	CCD	MARMOSAIC 225 mm CCD		2008-08-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.0000	APS	22-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	30	99.3	0.089	14.42			13710		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.45	98.2		0.298	6.93

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	PDB entry 1P5Z	2.31	30	11826	1310	95.16	0.21041	0.2049	0.26108	RANDOM	45.265

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]
1.31			1.31		-2.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.044
r_dihedral_angle_3_deg	18.256
r_dihedral_angle_4_deg	15.173
r_dihedral_angle_1_deg	5.261
r_scangle_it	3.055
r_scbond_it	1.983
r_mcangle_it	1.475
r_angle_refined_deg	1.402
r_mcbond_it	0.85
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.218
r_xyhbond_nbd_refined	0.217
r_nbd_refined	0.216
r_symmetry_hbond_refined	0.164
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1838
Nucleic Acid Atoms
Solvent Atoms	91
Heterogen Atoms	44

Software

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