1Q91

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor DPB-T


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MH9pdb code 1MH9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.3298PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.651α = 90
b = 73.651β = 90
c = 106.83γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-01-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

Data Collection

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb code 1MH91.619.773848438484385997.70.1860.1860.206RANDOM26
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]
-1.62-1.623.25
RMS Deviations
KeyRefinement Restraint Deviation
c_scbond_it26.96
c_dihedral_angle_d23.9
c_scangle_it14.32
c_mcangle_it3.77
c_mcbond_it3.04
c_angle_deg2.2
c_improper_angle_d1.48
c_bond_d0.026
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1598
Nucleic Acid Atoms
Solvent Atoms328
Heterogen Atoms34

Software

Software
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing