1ZMX | pdb_00001zmx

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1OT3	PDB entry 1OT3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION	6.5	288	MES, lithium sulphate, mPEG 2000, pH 6.5, Counter diffusion, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.712	α = 90
b = 70.34	β = 90.69
c = 224.528	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	Mirrors	2003-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.939	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	3.1	41.17	99.9				39975	1	1

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)
	3.1	3.27	99.9		0.38	3.4	3.7	39562

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 1OT3	3.1	41.17	1	37947	2005	99.96	0.2696	0.26958	0.26858	0.24	0.2884	0.26	RANDOM	37.441

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]
-0.9		2.48	2.32		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.314
r_scangle_it	2.254
r_scbond_it	1.247
r_mcangle_it	1.212
r_angle_refined_deg	1.134
r_mcbond_it	0.635
r_symmetry_hbond_refined	0.458
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.134

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.314
r_scangle_it	2.254
r_scbond_it	1.247
r_mcangle_it	1.212
r_angle_refined_deg	1.134
r_mcbond_it	0.635
r_symmetry_hbond_refined	0.458
r_symmetry_vdw_refined	0.313
r_nbd_refined	0.202
r_xyhbond_nbd_refined	0.134
r_chiral_restr	0.09
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12536
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	176

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.