1Z4M

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

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5		pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.8	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.572	α = 90
b = 73.572	β = 90
c = 105.748	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		CCD			2004-01-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.7	40	98.5	0.047	24.5	5		32144

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	1.7	1.76	98.3		0.334	3.7

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	1.7	40	30463	1624	98.49	0.19403	0.19291	0.21527	RANDOM	24.348

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]
-0.28			-0.28		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.469
r_dihedral_angle_4_deg	16.438
r_dihedral_angle_3_deg	13.953
r_dihedral_angle_1_deg	5.866
r_scangle_it	3.935
r_scbond_it	2.554
r_mcangle_it	1.739
r_angle_refined_deg	1.631
r_mcbond_it	1.051
r_nbtor_refined	0.316
r_symmetry_vdw_refined	0.244
r_nbd_refined	0.212
r_symmetry_hbond_refined	0.137
r_chiral_restr	0.105
r_xyhbond_nbd_refined	0.105
r_bond_refined_d	0.015
r_metal_ion_refined	0.009
r_gen_planes_refined	0.007
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1597
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement