☰ Navigation Tabs
Structure of the major pilus backbone protein from Streptococcus Agalactiae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2X9W PDB ENTRY 2X9W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 25% PEG4K, 0.1M HEPES PH 7.2, 90 MM POTASSIUM SODIUM TARTRATE
Crystal Properties Matthews coefficient Solvent content 2.63 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.863 α = 90 b = 104.681 β = 90 c = 159.25 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 ADSC CCD 2009-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 1.75 40 100 0.1 14.9 9.6 108305 2 18.6
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 1.75 1.84 100 0.6 3.7 9.6
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 PDB ENTRY 2X9W 1.75 40 102811 5403 99.98 0.1864 0.18489 0.2522 0.21588 0.2825 RANDOM 31.831
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] -0.98 0.58 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 13.509 r_dihedral_angle_3_deg 12.672 r_dihedral_angle_1_deg 5.997 r_scangle_it 2.081 r_scbond_it 1.237 r_angle_refined_deg 1.048 r_angle_other_deg 0.745 r_mcangle_it 0.725 r_mcbond_it 0.379
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.836 r_dihedral_angle_4_deg 13.509 r_dihedral_angle_3_deg 12.672 r_dihedral_angle_1_deg 5.997 r_scangle_it 2.081 r_scbond_it 1.237 r_angle_refined_deg 1.048 r_angle_other_deg 0.745 r_mcangle_it 0.725 r_mcbond_it 0.379 r_mcbond_other 0.093 r_chiral_restr 0.064 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6929 Nucleic Acid Atoms Solvent Atoms 895 Heterogen Atoms 3
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling MOLREP phasing