4YIH

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4L57PDB ENTRY 4L57

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429340 mM potassium phosphate monobasic, 6% PEG8000, 20% gycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.818α = 111.18
b = 46.451β = 88.16
c = 61.738γ = 104.7
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.8257.44395.80.04612.272.1133500-334.274
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.821.9394.10.4622.09

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 4L571.8257.4433458167296.110.18680.18470.2278RANDOM36.8837
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]
-0.82-0.58-0.20.690.87-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.563
r_dihedral_angle_4_deg19.675
r_dihedral_angle_3_deg13.029
r_dihedral_angle_1_deg6.248
r_mcangle_it2.693
r_angle_refined_deg2.083
r_mcbond_it1.987
r_mcbond_other1.985
r_angle_other_deg1.256
r_chiral_restr0.171
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.563
r_dihedral_angle_4_deg19.675
r_dihedral_angle_3_deg13.029
r_dihedral_angle_1_deg6.248
r_mcangle_it2.693
r_angle_refined_deg2.083
r_mcbond_it1.987
r_mcbond_other1.985
r_angle_other_deg1.256
r_chiral_restr0.171
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.006
r_gen_planes_other0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3066
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms84

Software

Software
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
XDSdata scaling