2IZO

Structure of an Archaeal PCNA1-PCNA2-FEN1 Complex


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROPPRIOR TO CRYSTALLISATION THE PCNA1-PCNA2-PCNA3 COMPLEX WAS MIXED WITH FEN1 AT AN EQUIMOLAR RATIO AND INCUBATED FOR 20 MIN AT 294 K. PCNA1-PCNA2-FEN1 CO-CRYSTALS WERE GROWN BY THE VAPOUR DIFFUSION METHOD IN HANGING DROPS. PCNA3 WAS NOT PRESENT IN THE CRYSTAL LATTICE. DROPS WERE PREPARED BY MIXING 100 MM PROTEIN COMPLEX IN 20 MM TRIS-HCL PH 8.0, 200 MM NACL, 5 MM MGCL2, 2 MM DTT BUFFER SOLUTION WITH EQUAL VOLUMES OF 0.1M ACETATE PH 4.8, 8% PEG 8,000, 220 MM ZNOAC2 AND 30 MM GLYCYL-GLYCYL-GLYCINE.
Crystal Properties
Matthews coefficientSolvent content
2.4550

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.986α = 90
b = 99.774β = 90
c = 99.958γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2005-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.86099.30.0815.34.82353471.32
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)
12.82.9599.80.5734.9

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 1B43 FOR FEN1 AND 1VYJ FOR PCNA1 AND PCNA22.93020108108898.90.2530.250.312RANDOM49.71
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]
0.55-4.113.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.938
r_dihedral_angle_3_deg17.26
r_dihedral_angle_4_deg16.199
r_dihedral_angle_1_deg5.27
r_angle_refined_deg1.031
r_scangle_it0.746
r_scbond_it0.436
r_symmetry_hbond_refined0.387
r_mcangle_it0.319
r_nbtor_refined0.301
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.938
r_dihedral_angle_3_deg17.26
r_dihedral_angle_4_deg16.199
r_dihedral_angle_1_deg5.27
r_angle_refined_deg1.031
r_scangle_it0.746
r_scbond_it0.436
r_symmetry_hbond_refined0.387
r_mcangle_it0.319
r_nbtor_refined0.301
r_symmetry_vdw_refined0.232
r_nbd_refined0.197
r_mcbond_it0.185
r_xyhbond_nbd_refined0.151
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5725
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms8

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing