2ZVK

Crystal structure of PCNA in complex with DNA polymerase eta fragment


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
13.6293pH3.6, HANGING DROP VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.7855.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.027α = 90
b = 82.027β = 90
c = 310.443γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210Rhodium coated silicon single crystal mirrors2005-10-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1Photon FactoryAR-NW12A

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
12.75092.10.0938.12.527933-0.459
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)
12.72.881.30.3282.62

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 1VYM2.7202644013981000.218380.214890.28582RANDOM30.089
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]
-0.02-0.020.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.829
r_dihedral_angle_4_deg27.632
r_dihedral_angle_3_deg22.066
r_dihedral_angle_1_deg7.874
r_scangle_it3.278
r_scbond_it2
r_angle_refined_deg1.902
r_mcangle_it1.412
r_angle_other_deg1.273
r_mcbond_it0.822
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.829
r_dihedral_angle_4_deg27.632
r_dihedral_angle_3_deg22.066
r_dihedral_angle_1_deg7.874
r_scangle_it3.278
r_scbond_it2
r_angle_refined_deg1.902
r_mcangle_it1.412
r_angle_other_deg1.273
r_mcbond_it0.822
r_chiral_restr0.096
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_gen_planes_other0.007
r_mcbond_other0.005
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6003
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing