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Crystal structure of the complex of proliferating cell nuclear antigen (PCNA) from Leishmania donovani with 1,5-Bis (4-amidinophenoxy) pentane (PNT) at 2.95 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 20% PEG 3350, 200mM sodium malonate
Crystal Properties Matthews coefficient Solvent content 4.38 71.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.024 α = 90 b = 150.664 β = 90 c = 170.547 γ = 90
Symmetry Space Group P 21 21 21
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 MARRESEARCH 2015-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.95 43.49 98.8 0.12 11.6 4.9 72691
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) 1 2.95 3.03 84.52 0.49 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5B7O 2.954 43.485 72691 1437 98.807 0.212 0.211 0.2143 0.2567 0.253 90.593
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] 0.136 0.044 -0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.76 r_lrange_it 19.41 r_lrange_other 19.41 r_scangle_it 14.274 r_scangle_other 14.274 r_dihedral_angle_3_deg 12.375 r_mcangle_it 11.062 r_mcangle_other 11.062 r_dihedral_angle_4_deg 10.342 r_scbond_it 9.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.76 r_lrange_it 19.41 r_lrange_other 19.41 r_scangle_it 14.274 r_scangle_other 14.274 r_dihedral_angle_3_deg 12.375 r_mcangle_it 11.062 r_mcangle_other 11.062 r_dihedral_angle_4_deg 10.342 r_scbond_it 9.336 r_scbond_other 9.33 r_mcbond_other 7.425 r_mcbond_it 7.424 r_dihedral_angle_1_deg 5.864 r_angle_other_deg 2.291 r_dihedral_angle_other_2_deg 1.815 r_angle_refined_deg 1.31 r_nbd_other 0.505 r_symmetry_nbd_refined 0.468 r_symmetry_xyhbond_nbd_refined 0.359 r_symmetry_nbd_other 0.231 r_nbd_refined 0.218 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.133 r_symmetry_xyhbond_nbd_other 0.078 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.05 r_bond_other_d 0.035 r_bond_refined_d 0.007 r_gen_planes_other 0.006 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11514 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing