1Z4I

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with deoxyribouridine 5'-monophosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	293	PEG8000, potassium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.7	α = 90
b = 73.7	β = 90
c = 106.42	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	ADSC QUANTUM 4		2003-11-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	1.98	20	100	0.08	23.6	15.1	21094	21057

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	1.98	2.1	98.8		0.36	7.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.98	20	21094	19972	1082	99.98	0.16564	0.16355	0.20608	RANDOM	26.509

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]
-0.43			-0.43		0.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.245
r_scangle_it	4.702
r_scbond_it	2.921
r_mcangle_it	2.107
r_angle_refined_deg	1.69
r_mcbond_it	1.116
r_angle_other_deg	0.933
r_symmetry_vdw_other	0.314
r_nbd_other	0.254
r_nbd_refined	0.211
r_symmetry_hbond_refined	0.159
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.104
r_symmetry_vdw_refined	0.088
r_nbtor_other	0.086
r_bond_refined_d	0.019
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1597
Nucleic Acid Atoms
Solvent Atoms	194
Heterogen Atoms	27

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
XDS	data scaling
CNS	phasing