6G2L

Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PMTMU


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YIK 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829120 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4,
Crystal Properties
Matthews coefficientSolvent content
3.1260.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.797α = 90
b = 73.797β = 90
c = 106.632γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2016-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
11.4846.8899.50.070.99916.047.774937826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.481.5796.80.8020.7932.057.89

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT4YIK1.4846.8748259111699.460.12240.12180.1496RANDOM23.459
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]
-0.2-0.20.4
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.17
r_sphericity_free20.442
r_rigid_bond_restr14.721
r_dihedral_angle_4_deg13.898
r_dihedral_angle_3_deg11.584
r_sphericity_bonded8.758
r_dihedral_angle_1_deg5.633
r_angle_other_deg1.974
r_angle_refined_deg1.83
r_chiral_restr0.175
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.17
r_sphericity_free20.442
r_rigid_bond_restr14.721
r_dihedral_angle_4_deg13.898
r_dihedral_angle_3_deg11.584
r_sphericity_bonded8.758
r_dihedral_angle_1_deg5.633
r_angle_other_deg1.974
r_angle_refined_deg1.83
r_chiral_restr0.175
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_gen_planes_other0.007
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1614
Nucleic Acid Atoms
Solvent Atoms300
Heterogen Atoms66

Software

Software
Software NamePurpose
XDSdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction