6G22

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


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
3.2361.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.753α = 90
b = 73.753β = 90
c = 106.563γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2016-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5419

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
11.8543.1997.90.0580.99915.033.354702830.2
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)
11.851.9697.30.5880.7081.461.77

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 SYNTHESISTHROUGHOUT4YIK1.8543.1924012126497.840.157060.155340.19069RANDOM27.376
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]
-0.28-0.280.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.624
r_dihedral_angle_4_deg15.421
r_dihedral_angle_3_deg12.918
r_long_range_B_refined6.338
r_long_range_B_other6.142
r_dihedral_angle_1_deg5.703
r_scangle_other4.724
r_mcangle_it3.297
r_mcangle_other3.297
r_scbond_it3.131
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.624
r_dihedral_angle_4_deg15.421
r_dihedral_angle_3_deg12.918
r_long_range_B_refined6.338
r_long_range_B_other6.142
r_dihedral_angle_1_deg5.703
r_scangle_other4.724
r_mcangle_it3.297
r_mcangle_other3.297
r_scbond_it3.131
r_scbond_other3.13
r_mcbond_it2.349
r_mcbond_other2.34
r_angle_refined_deg1.794
r_angle_other_deg0.982
r_chiral_restr0.161
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1584
Nucleic Acid Atoms
Solvent Atoms236
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PDB_EXTRACTdata extraction