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Structure of split monoubiquitinated PCNA with ubiquitin in position two
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PLQ pdb entry 1PLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 291 2.04 M ammonium sulfate, 0.1 M sodium citrate, 3% ethanol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.04 69.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.516 α = 90 b = 122.516 β = 90 c = 122.516 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD NOIR-1 saggitally focused mirrors 2009-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.97 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.8 86.63 100 0.109 10.5 8.74 15333 2 88.237
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.8 2.9 100 0.604 2.4 5.38 1471
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 1PLQ 2.8 86 2 15333 14567 766 100 0.279 0.279 0.277 0.2937 0.314 0.3249 RANDOM 84.621
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.385 r_dihedral_angle_3_deg 21.312 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_1_deg 7.03 r_scangle_it 3.183 r_scbond_it 1.769 r_angle_refined_deg 1.587 r_mcangle_it 1.525 r_mcbond_it 0.81 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.385 r_dihedral_angle_3_deg 21.312 r_dihedral_angle_4_deg 20.377 r_dihedral_angle_1_deg 7.03 r_scangle_it 3.183 r_scbond_it 1.769 r_angle_refined_deg 1.587 r_mcangle_it 1.525 r_mcbond_it 0.81 r_chiral_restr 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2590 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose PHASER phasing REFMAC refinement PDB_EXTRACT data extraction StructureStudio data collection d*TREK data reduction d*TREK data scaling