1ZM7

Crystal structure of D. melanogaster deoxyribonucleoside kinase mutant N64D in complex with dTTP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	288	MES, lithium sulphate, mPEG 2000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.04	α = 90
b = 119.27	β = 92.59
c = 68.388	γ = 90

Symmetry
Space Group	P 1 21 1

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	ADSC QUANTUM 4		2003-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	1.0	ESRF	ID14-4

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	2.2	44.72	99.9				65654	1	1

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)
	2.2	2.32	99.9		0.07	4.1	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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 1OE0	2.2	44.72	1	65654	51654	2763	99.94	0.21329	0.21202	0.23695	RANDOM	36.736

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]
-0.22		0.54	-2.4		2.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.422
r_scangle_it	4.151
r_scbond_it	2.454
r_mcangle_it	1.639
r_angle_refined_deg	1.274
r_mcbond_it	0.831
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.185
r_metal_ion_refined	0.154

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.422
r_scangle_it	4.151
r_scbond_it	2.454
r_mcangle_it	1.639
r_angle_refined_deg	1.274
r_mcbond_it	0.831
r_symmetry_vdw_refined	0.247
r_nbd_refined	0.202
r_symmetry_hbond_refined	0.185
r_metal_ion_refined	0.154
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6576
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	117

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.