☰ Navigation Tabs
Crystal Structure of shaft pilin PilA from Streptococcus sanguinis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8WGG PilB protein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.1 M HEPES pH 7.5, 0.01 M Cadmium Sulphate, 1.0 M Sodium acetate tri-hydrate.
Crystal Properties Matthews coefficient Solvent content 3.01 59.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.593 α = 90 b = 89.949 β = 90 c = 216.408 γ = 90
Symmetry Space Group P 2 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 6M 2023-04-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.8856 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.995 58.35 69 0.094 0.054 0.989 7.8 3.8 36257 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.995 2.159 90.5 0.543 0.379 0.592 2.8
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 THROUGHOUT 1.995 58.35 34403 1854 87.8 0.21184 0.2093 0.2163 0.25936 0.2632 RANDOM 32.359
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] -0.47 0.33 0.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.407 r_dihedral_angle_4_deg 18.856 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 8.088 r_long_range_B_refined 6.415 r_long_range_B_other 6.415 r_scangle_other 3.211 r_mcangle_it 3.096 r_mcangle_other 3.096 r_angle_other_deg 2.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.407 r_dihedral_angle_4_deg 18.856 r_dihedral_angle_3_deg 14.564 r_dihedral_angle_1_deg 8.088 r_long_range_B_refined 6.415 r_long_range_B_other 6.415 r_scangle_other 3.211 r_mcangle_it 3.096 r_mcangle_other 3.096 r_angle_other_deg 2.811 r_scbond_it 1.914 r_scbond_other 1.914 r_mcbond_it 1.783 r_mcbond_other 1.783 r_angle_refined_deg 1.726 r_chiral_restr 0.07 r_gen_planes_other 0.044 r_bond_other_d 0.037 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 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 6412 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 29
Software Software Software Name Purpose XDS data reduction PHASER phasing Coot model building REFMAC refinement Aimless data scaling