3V60

Structure of S. cerevisiae PCNA conjugated to SUMO on lysine 164


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52914% PEG 8000, 500 mM LiSO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
5.276.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 268.126α = 90
b = 268.126β = 90
c = 268.126γ = 90
Symmetry
Space GroupF 4 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-06-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9792APS24-ID-C

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
12.65099.70.05221.712.231461025873
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)
12.62.6999.20.3636.92488

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 entries 1PLQ and 1EUV2.65025738130799.170.21220.21030.2492RANDOM62.2473
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.099
r_dihedral_angle_3_deg19.746
r_dihedral_angle_4_deg17.952
r_dihedral_angle_1_deg6.651
r_scangle_it4.122
r_scbond_it2.341
r_mcangle_it1.922
r_angle_refined_deg1.454
r_mcbond_it0.997
r_chiral_restr0.101
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.099
r_dihedral_angle_3_deg19.746
r_dihedral_angle_4_deg17.952
r_dihedral_angle_1_deg6.651
r_scangle_it4.122
r_scbond_it2.341
r_mcangle_it1.922
r_angle_refined_deg1.454
r_mcbond_it0.997
r_chiral_restr0.101
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2646
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms30

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
MOLREPphasing