1Z4Q

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.5pH 4.5
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.77α = 90
b = 73.77β = 90
c = 106.057γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCD2004-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.052099.70.07321.56.118971
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.121000.3764.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.05201797097699.840.176010.174170.21032RANDOM25.206
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]
-0.6-0.61.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.519
r_scangle_it4.721
r_scbond_it2.986
r_mcangle_it2.018
r_angle_refined_deg1.672
r_mcbond_it1.11
r_angle_other_deg0.936
r_symmetry_vdw_other0.375
r_xyhbond_nbd_refined0.317
r_symmetry_vdw_refined0.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.519
r_scangle_it4.721
r_scbond_it2.986
r_mcangle_it2.018
r_angle_refined_deg1.672
r_mcbond_it1.11
r_angle_other_deg0.936
r_symmetry_vdw_other0.375
r_xyhbond_nbd_refined0.317
r_symmetry_vdw_refined0.283
r_nbd_other0.256
r_nbd_refined0.218
r_symmetry_hbond_refined0.149
r_chiral_restr0.111
r_nbtor_other0.088
r_bond_refined_d0.02
r_gen_planes_other0.016
r_gen_planes_refined0.012
r_metal_ion_refined0.008
r_bond_other_d0.002
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 AtomsNumber
Protein Atoms1597
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms22

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement