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Crystal structure of proliferating cell nuclear antigen from Leishmania donovani at 2.73 Angstrom 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, sodium malonate
Crystal Properties Matthews coefficient Solvent content 4.38 76.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.8 α = 90 b = 149.574 β = 90 c = 169.245 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 MIRROR 2016-06-28 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) 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 2.73 112.08 90.7 12 2.9 89366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.73 2.78 80 1.45
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5B7O 2.73 112.08 89366 927 99.31 0.19783 0.19742 0.2016 0.23915 0.242 RANDOM 92.614
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] 1.91 0.89 -2.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 22.629 r_dihedral_angle_3_deg 22.107 r_long_range_B_refined 19.395 r_long_range_B_other 19.395 r_scangle_other 15.803 r_mcangle_it 12.951 r_mcangle_other 12.951 r_scbond_it 11.118 r_scbond_other 11.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.793 r_dihedral_angle_4_deg 22.629 r_dihedral_angle_3_deg 22.107 r_long_range_B_refined 19.395 r_long_range_B_other 19.395 r_scangle_other 15.803 r_mcangle_it 12.951 r_mcangle_other 12.951 r_scbond_it 11.118 r_scbond_other 11.118 r_mcbond_it 9.314 r_mcbond_other 9.313 r_dihedral_angle_1_deg 8.532 r_angle_refined_deg 2.296 r_angle_other_deg 1.214 r_chiral_restr 0.154 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 11514 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing