☰ Navigation Tabs
Roll out the beta-barrel: structure and mechanism of Pac13, a unique nucleoside dehydratase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NJN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.8 293 0.1 M Tris pH 8.8,
20% w/v PEG8K,
0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.52 51.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.49 α = 90 b = 66.49 β = 90 c = 54.71 γ = 120
Symmetry Space Group P 32 2 1
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 PILATUS 6M 2015-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9797 Diamond I03
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 1.55 57.58 100 0.059 23.5 10.9 20630 18.63
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 1.55 1.61 99.9 0.776 10.6
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 5NJN 1.55 57.58 19574 1056 99.97 0.18099 0.17994 0.1907 0.20115 0.2069 RANDOM 21.958
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] 0.16 0.08 0.16 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.481 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_3_deg 12.328 r_long_range_B_refined 8.234 r_dihedral_angle_1_deg 6.948 r_long_range_B_other 6.677 r_scangle_other 2.872 r_scbond_it 1.765 r_scbond_other 1.763 r_mcangle_it 1.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.481 r_dihedral_angle_4_deg 15.57 r_dihedral_angle_3_deg 12.328 r_long_range_B_refined 8.234 r_dihedral_angle_1_deg 6.948 r_long_range_B_other 6.677 r_scangle_other 2.872 r_scbond_it 1.765 r_scbond_other 1.763 r_mcangle_it 1.625 r_mcangle_other 1.624 r_angle_refined_deg 1.272 r_mcbond_it 0.991 r_mcbond_other 0.988 r_angle_other_deg 0.709 r_chiral_restr 0.08 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 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 976 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction xia2 data reduction SCALA data scaling PHASER phasing