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Crystal structure of C-terminal domain of shaft pilin spaA from Lactobacillus rhamnosus GG, - I422 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PHS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 295 0.1M sodium acetate, 25% PEG400
Crystal Properties Matthews coefficient Solvent content 1.18 53.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.24 α = 90 b = 100.24 β = 90 c = 57.539 γ = 90
Symmetry Space Group I 4 2 2
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 2012-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97625 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 1.6 28.89 99.9 0.071 37 28.5 19599
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 1.6 1.75 99.7 0.604 6.4 29.1
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 3PHS 1.6 28.89 18598 1001 99.77 0.1311 0.12972 0.129 0.15769 0.1562 RANDOM 19.556
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] -0.05 -0.05 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.183 r_sphericity_free 26.786 r_dihedral_angle_3_deg 9.446 r_sphericity_bonded 9.24 r_dihedral_angle_4_deg 7.676 r_dihedral_angle_1_deg 6.499 r_long_range_B_refined 3.542 r_long_range_B_other 3.54 r_scangle_other 2.03 r_rigid_bond_restr 1.898
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.183 r_sphericity_free 26.786 r_dihedral_angle_3_deg 9.446 r_sphericity_bonded 9.24 r_dihedral_angle_4_deg 7.676 r_dihedral_angle_1_deg 6.499 r_long_range_B_refined 3.542 r_long_range_B_other 3.54 r_scangle_other 2.03 r_rigid_bond_restr 1.898 r_scbond_it 1.586 r_scbond_other 1.585 r_mcangle_other 1.518 r_mcangle_it 1.517 r_angle_refined_deg 1.221 r_mcbond_it 1.174 r_mcbond_other 1.165 r_angle_other_deg 0.69 r_chiral_restr 0.07 r_bond_refined_d 0.008 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 931 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data processing Aimless data scaling MR-Rosetta phasing Coot model building