4YIK

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 4L6APDB ENTRY 4L6A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP429320 mM potassium phosphate monobasic, 8% PEG8000, 10% gycerol, pH 4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.1360.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.87α = 90
b = 73.87β = 90
c = 106.19γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-06-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.915BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.48360.6411000.06515.384943849438
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4831.561000.7450.74517.67108

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 SYNTHESISTHROUGHOUTPDB ENTRY 4L6A1.48360.6449321249799.890.1540.15280.1758RANDOM22.5767
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]
-0.39-0.390.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.691
r_dihedral_angle_4_deg16.707
r_dihedral_angle_3_deg12.117
r_dihedral_angle_1_deg6.155
r_mcangle_it2.377
r_angle_refined_deg1.935
r_mcbond_it1.539
r_mcbond_other1.538
r_angle_other_deg0.885
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.691
r_dihedral_angle_4_deg16.707
r_dihedral_angle_3_deg12.117
r_dihedral_angle_1_deg6.155
r_mcangle_it2.377
r_angle_refined_deg1.935
r_mcbond_it1.539
r_mcbond_other1.538
r_angle_other_deg0.885
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1636
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms92

Software

Software
Software NamePurpose
PDB_EXTRACTdata extraction
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing