☰ Navigation Tabs
Crystal structure of basal pilin PilB from Streptococcus sanguinis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WG6 SeMet derivative of same protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 295 0.1 M Tris pH 8.5, 8% (w/v) PEG 4000 and 0.8 M Lithium Chloride
Crystal Properties Matthews coefficient Solvent content 2.4 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.911 α = 90 b = 58.63 β = 90 c = 212.985 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 PILATUS 2M 2022-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8713128 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.878 45.207 94.5 0.055 0.995 9.3 8.9 30356 21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.878 1.937 92.3 0.317 0.887 2.8 9.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 FREE R-VALUE 1.88 45.2 28866 1490 77.97 0.19917 0.19762 0.2061 0.229 0.239 RANDOM 18.3
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] -0.09 -0.47 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.756 r_dihedral_angle_1_deg 6.567 r_dihedral_angle_2_deg 5.186 r_long_range_B_refined 4.431 r_long_range_B_other 4.279 r_scangle_other 1.873 r_mcangle_it 1.23 r_mcangle_other 1.23 r_scbond_it 1.154 r_scbond_other 1.154
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.756 r_dihedral_angle_1_deg 6.567 r_dihedral_angle_2_deg 5.186 r_long_range_B_refined 4.431 r_long_range_B_other 4.279 r_scangle_other 1.873 r_mcangle_it 1.23 r_mcangle_other 1.23 r_scbond_it 1.154 r_scbond_other 1.154 r_angle_refined_deg 1.099 r_mcbond_other 0.757 r_mcbond_it 0.755 r_angle_other_deg 0.352 r_chiral_restr 0.044 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 3175 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms 41
Software Software Software Name Purpose autoPROC data reduction MOLREP phasing Coot model building REFMAC refinement