1Z4M

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


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 = 73.572α = 90
b = 73.572β = 90
c = 105.748γ = 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
11.74098.50.04724.5532144
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)
11.71.7698.30.3343.7

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 REPLACEMENTTHROUGHOUT1.74030463162498.490.194030.192910.21527RANDOM24.348
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]
-0.28-0.280.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.469
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg13.953
r_dihedral_angle_1_deg5.866
r_scangle_it3.935
r_scbond_it2.554
r_mcangle_it1.739
r_angle_refined_deg1.631
r_mcbond_it1.051
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.469
r_dihedral_angle_4_deg16.438
r_dihedral_angle_3_deg13.953
r_dihedral_angle_1_deg5.866
r_scangle_it3.935
r_scbond_it2.554
r_mcangle_it1.739
r_angle_refined_deg1.631
r_mcbond_it1.051
r_nbtor_refined0.316
r_symmetry_vdw_refined0.244
r_nbd_refined0.212
r_symmetry_hbond_refined0.137
r_chiral_restr0.105
r_xyhbond_nbd_refined0.105
r_bond_refined_d0.015
r_metal_ion_refined0.009
r_gen_planes_refined0.007
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 AtomsNumber
Protein Atoms1597
Nucleic Acid Atoms
Solvent Atoms163
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement