2JAR

Crystal structure of D12N variant of mouse cytosolic 5'(3')- deoxyribonucleotidase (cdN) in complex with deoxyuridine 5'- monophosphate

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	279	0.2 M MAGNESIUM CHLORIDE, 0.1 M BIS-TRIS PH 5.5, 23-25% PEG3350 AT 6 DEGREES CELSIUS

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 75.309	α = 90
b = 75.309	β = 90
c = 85.174	γ = 120

Symmetry
Space Group	P 62

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 CCD	MIRRORS	2006-02-25	M	SINGLE WAVELENGTH

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

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	1.95	65.23	100	0.1	19	10.7		20062

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)
1	1.95	2.06	100		0.34	5.8	10.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.94	40	19307	1034	100	0.158	0.156	0.201	RANDOM	24.74

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]
-0.05	-0.03		-0.05		0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.997
r_dihedral_angle_4_deg	17.138
r_dihedral_angle_3_deg	13.849
r_dihedral_angle_1_deg	6.041
r_scangle_it	3.685
r_scbond_it	3.233
r_mcangle_it	1.727
r_angle_refined_deg	1.423
r_mcbond_it	1.201
r_nbtor_refined	0.302
r_nbd_refined	0.191
r_symmetry_vdw_refined	0.188
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.139
r_chiral_restr	0.1
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1595
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	21

Software

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