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Crystal structure of the complex of Proliferating Cell Nuclear Antigen from Leishmania donovani with arginine at 3.19 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J0J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 20% PEG 3350, sodium malonate
Crystal Properties Matthews coefficient Solvent content 4.4 76.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.926 α = 90 b = 150.588 β = 90 c = 171.009 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 PIXEL DECTRIS PILATUS3 2M 2018-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-1 0.966 ESRF MASSIF-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 3.19 106.63 99.38 0.053 0.06 0.028 0.999 16.3 4.6 58894
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.19 3.24 99.8 0.653 0.732 0.323 0.752 2.2 5
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6J0J 3.19 106.63 55874 3020 99.38 0.17011 0.16694 0.22695 0.2278 RANDOM 110.526
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] 4.94 0.1 -5.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.403 r_dihedral_angle_3_deg 23.143 r_long_range_B_refined 20.601 r_long_range_B_other 20.6 r_dihedral_angle_4_deg 18.166 r_scangle_other 17.336 r_mcangle_it 14.783 r_mcangle_other 14.782 r_scbond_it 11.586 r_scbond_other 11.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.403 r_dihedral_angle_3_deg 23.143 r_long_range_B_refined 20.601 r_long_range_B_other 20.6 r_dihedral_angle_4_deg 18.166 r_scangle_other 17.336 r_mcangle_it 14.783 r_mcangle_other 14.782 r_scbond_it 11.586 r_scbond_other 11.585 r_mcbond_it 10.278 r_mcbond_other 10.276 r_dihedral_angle_1_deg 10.169 r_angle_refined_deg 1.727 r_angle_other_deg 1.229 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11605 Nucleic Acid Atoms Solvent Atoms 73 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building