1Z4J

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with uridine 2'-monophosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293PEG8000, potassium dihydrogen phosphate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.453α = 90
b = 73.453β = 90
c = 106.085γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2004-01-27MSINGLE 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
11.84098.40.06127.38.227294
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)
11.81.8698.80.374.7

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 REPLACEMENTTHROUGHOUT1.84025876136998.430.173980.172480.2018RANDOM20.844
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]
-0.35-0.350.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.312
r_scangle_it4.365
r_scbond_it2.787
r_mcangle_it1.839
r_angle_refined_deg1.614
r_mcbond_it1.026
r_angle_other_deg0.904
r_symmetry_vdw_other0.351
r_symmetry_vdw_refined0.257
r_nbd_other0.249
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.312
r_scangle_it4.365
r_scbond_it2.787
r_mcangle_it1.839
r_angle_refined_deg1.614
r_mcbond_it1.026
r_angle_other_deg0.904
r_symmetry_vdw_other0.351
r_symmetry_vdw_refined0.257
r_nbd_other0.249
r_nbd_refined0.217
r_symmetry_hbond_refined0.116
r_chiral_restr0.113
r_xyhbond_nbd_refined0.094
r_nbtor_other0.086
r_metal_ion_refined0.074
r_bond_refined_d0.017
r_gen_planes_other0.011
r_gen_planes_refined0.01
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 Atoms157
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing