1Z4J | pdb_00001z4j

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-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 = 73.453	α = 90
b = 73.453	β = 90
c = 106.085	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			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	1.8	40	98.4	0.061	27.3	8.2		27294

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	1.8	1.86	98.8		0.37	4.7

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	40	25876	1369	98.43	0.17398	0.17248	0.19	0.2018	0.21	RANDOM	20.844

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]
-0.35			-0.35		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.312
r_scangle_it	4.365
r_scbond_it	2.787
r_mcangle_it	1.839
r_angle_refined_deg	1.614
r_mcbond_it	1.026
r_angle_other_deg	0.904
r_symmetry_vdw_other	0.351
r_symmetry_vdw_refined	0.257
r_nbd_other	0.249
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.113
r_xyhbond_nbd_refined	0.094
r_nbtor_other	0.086
r_metal_ion_refined	0.074
r_bond_refined_d	0.017
r_gen_planes_other	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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	157
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing