1Z4Q | pdb_00001z4q

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with 2',3'-dideoxy-2',3-didehydrothymidine 5'-monophosphate (d4T-MP)

X-RAY DIFFRACTION

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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 = 73.77	α = 90
b = 73.77	β = 90
c = 106.057	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	2.05	20	99.7	0.073	21.5	6.1		18971

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)
	2.05	2.12	100		0.376	4.3

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	2.05	20	17970	976	99.84	0.17601	0.17417	0.18	0.21032	0.22	RANDOM	25.206

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]
-0.6			-0.6		1.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.519
r_scangle_it	4.721
r_scbond_it	2.986
r_mcangle_it	2.018
r_angle_refined_deg	1.672
r_mcbond_it	1.11
r_angle_other_deg	0.936
r_symmetry_vdw_other	0.375
r_xyhbond_nbd_refined	0.317
r_symmetry_vdw_refined	0.283
r_nbd_other	0.256
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.149
r_chiral_restr	0.111
r_nbtor_other	0.088
r_bond_refined_d	0.02
r_gen_planes_other	0.016
r_gen_planes_refined	0.012
r_metal_ion_refined	0.008
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	165
Heterogen Atoms	22

Software

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