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Crystal structure of shaft pilin spaD from Lactobacillus rhamnosus GG in bent conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YU5 5YU5, 5YXG experimental model PDB 5YXG 5YU5, 5YXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 30% PEG 1500
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.72 α = 90 b = 73.72 β = 90 c = 428.659 γ = 120
Symmetry Space Group P 65 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 2015-04-20 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) Rrim I (All) 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 2.51 71.55 89.6 0.14 0.148 0.048 0.997 10.6 9.1 19138 61.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.512 2.705 45.5 0.8 0.95 0.466 0.278 1.4 3.6
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 5YU5, 5YXG 2.51 71.55 18151 986 76.71 0.24325 0.24074 0.2473 0.29095 0.294 RANDOM 66
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] 0.18 0.09 0.18 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.553 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_4_deg 10.821 r_dihedral_angle_1_deg 6.461 r_long_range_B_refined 2.894 r_long_range_B_other 2.886 r_scangle_other 1.602 r_mcangle_it 1.561 r_mcangle_other 1.561 r_angle_refined_deg 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.553 r_dihedral_angle_3_deg 14.832 r_dihedral_angle_4_deg 10.821 r_dihedral_angle_1_deg 6.461 r_long_range_B_refined 2.894 r_long_range_B_other 2.886 r_scangle_other 1.602 r_mcangle_it 1.561 r_mcangle_other 1.561 r_angle_refined_deg 1.134 r_scbond_it 0.921 r_scbond_other 0.92 r_mcbond_other 0.905 r_mcbond_it 0.904 r_angle_other_deg 0.836 r_chiral_restr 0.066 r_bond_refined_d 0.006 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3189 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing