1Q92

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MH9PDB entry 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
2.6352.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.758α = 90
b = 73.758β = 90
c = 105.981γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.430209551
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.41.45

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 entry 1MH91.425.323752835599192964.830.135030.133370.16454RANDOM17.719
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]
0.160.16-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.325
r_sphericity_free5.48
r_scangle_it4.797
r_sphericity_bonded3.822
r_scbond_it3.304
r_mcangle_it2.586
r_rigid_bond_restr1.947
r_angle_refined_deg1.856
r_mcbond_it1.73
r_angle_other_deg1.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.325
r_sphericity_free5.48
r_scangle_it4.797
r_sphericity_bonded3.822
r_scbond_it3.304
r_mcangle_it2.586
r_rigid_bond_restr1.947
r_angle_refined_deg1.856
r_mcbond_it1.73
r_angle_other_deg1.008
r_nbd_refined0.501
r_symmetry_vdw_other0.385
r_symmetry_vdw_refined0.301
r_symmetry_hbond_refined0.29
r_nbd_other0.252
r_xyhbond_nbd_refined0.249
r_chiral_restr0.132
r_nbtor_other0.086
r_bond_refined_d0.02
r_gen_planes_other0.019
r_gen_planes_refined0.014
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1602
Nucleic Acid Atoms
Solvent Atoms326
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing