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Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E269A mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5F44
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2 M tri-Potassium citrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 4.09 69.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 228.632 α = 90 b = 63.033 β = 95.34 c = 104.904 γ = 90
Symmetry Space Group C 1 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 CCD MARMOSAIC 225 mm CCD 2015-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95372 ESRF BM14
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 2.39 80.79 99.5 0.066 16 5.1 59176
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 2.39 2.67 99.2 0.605 2.9 5.1
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 5F44 2.39 80.79 56110 2982 99.14 0.22002 0.21912 0.2227 0.23691 0.2389 RANDOM 62.394
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] -0.52 -0.9 1.95 -1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.638 r_dihedral_angle_3_deg 13.24 r_dihedral_angle_4_deg 10.418 r_long_range_B_refined 6.358 r_long_range_B_other 6.343 r_dihedral_angle_1_deg 6.237 r_scangle_other 2.883 r_mcangle_it 2.549 r_mcangle_other 2.549 r_scbond_it 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.638 r_dihedral_angle_3_deg 13.24 r_dihedral_angle_4_deg 10.418 r_long_range_B_refined 6.358 r_long_range_B_other 6.343 r_dihedral_angle_1_deg 6.237 r_scangle_other 2.883 r_mcangle_it 2.549 r_mcangle_other 2.549 r_scbond_it 1.81 r_scbond_other 1.809 r_mcbond_it 1.556 r_mcbond_other 1.556 r_angle_refined_deg 1.185 r_angle_other_deg 0.922 r_chiral_restr 0.066 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 6036 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing Coot model building