5ZUT

Crystal Structure of Yeast PCNA in Complex with N24 Peptide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6B8I6B8I, 5DA7
experimental modelPDB 5DA76B8I, 5DA7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5291n-Octyl-b-D-glu, NaCi pH 5.5, PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.8261.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.35α = 90
b = 84.03β = 93.62
c = 58.15γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-04-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.979SSRFBL17U1

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
12.8358.0398.70.1336.99212
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)
12.832.999.40.5127.2

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 REPLACEMENTTHROUGHOUT6B8I, 5DA72.8258.03868452798.40.33010.3260.3966RANDOM99.825
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]
67.58114.5-81.2413.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.033
r_dihedral_angle_4_deg22.145
r_dihedral_angle_3_deg20.118
r_dihedral_angle_1_deg8.837
r_mcangle_it5.734
r_mcbond_it3.493
r_mcbond_other3.49
r_angle_other_deg1.392
r_angle_refined_deg1.063
r_chiral_restr0.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.033
r_dihedral_angle_4_deg22.145
r_dihedral_angle_3_deg20.118
r_dihedral_angle_1_deg8.837
r_mcangle_it5.734
r_mcbond_it3.493
r_mcbond_other3.49
r_angle_other_deg1.392
r_angle_refined_deg1.063
r_chiral_restr0.043
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2155
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling