6T7Y

Structure of PCNA bound to cPIP motif of DP2 from P. abyssi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5AUJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.129330% PEG 400 0.2 M MgCl2 0.1M BIS-TRIS pH7.1
Crystal Properties
Matthews coefficientSolvent content
2.3748.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 140.736α = 90
b = 140.736β = 90
c = 38.521γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-11-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9793ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.770.3789.50.99915.85.26983
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7012.8630.21

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 REPLACEMENTTHROUGHOUT5auj2.770.37632366089.40.19290.18570.2621RANDOM134.05
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]
0.540.270.54-1.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_3_deg19.585
r_dihedral_angle_4_deg18.677
r_dihedral_angle_1_deg7.593
r_angle_refined_deg2.138
r_angle_other_deg1.18
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_gen_planes_other0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.635
r_dihedral_angle_3_deg19.585
r_dihedral_angle_4_deg18.677
r_dihedral_angle_1_deg7.593
r_angle_refined_deg2.138
r_angle_other_deg1.18
r_chiral_restr0.128
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_gen_planes_other0.011
r_bond_other_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1952
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
STARANISOdata scaling