2JAW

Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdN) in complex with 5-bromovinyldeoxyuridine 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	20% PEG8000, 0.050 M POTASSIUM DIHYDROGEN PHOSPHATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

Crystal Properties
Matthews coefficient	Solvent content
3.2	61.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.604	α = 90
b = 73.604	β = 90
c = 106.374	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	MARRESEARCH		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 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	40	99.4	0.06	20.5	5.7		21939

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	2.02	100		0.36	4.8

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	1.95	60.86	2079	1122	99.5	0.187	0.185	0.216	RANDOM	24.08

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]
-0.23			-0.23		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.496
r_dihedral_angle_4_deg	20.664
r_dihedral_angle_3_deg	13.899
r_dihedral_angle_1_deg	5.938
r_scangle_it	3.903
r_scbond_it	2.44
r_mcangle_it	1.53
r_angle_refined_deg	1.426
r_mcbond_it	0.88
r_nbtor_refined	0.314
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.158
r_symmetry_hbond_refined	0.126
r_chiral_restr	0.102
r_bond_refined_d	0.013
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	1599
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	25

Software

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