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Crystal structure of C-terminal fragment of SpaD from Lactobacillus rhamnosus GG generated by limited proteolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5YU5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.2 M ammonium chloride 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.22 44.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.106 α = 90 b = 83.16 β = 90 c = 149.403 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 MARMOSAIC 225 mm CCD 2014-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.95371 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 1.48 72.66 99.8 0.063 0.07 0.029 0.999 15.6 5.3 104530 16.2
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 1.48 1.62 99.8 0.536 0.596 0.253 0.813 3.2 5.2
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 SAD THROUGHOUT 5YU5 1.48 72.66 99221 5220 99.63 0.17807 0.17714 0.1783 0.19534 0.196 RANDOM 19.613
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] -1.01 0.05 0.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_3_deg 10.402 r_dihedral_angle_4_deg 9.084 r_dihedral_angle_1_deg 6.996 r_long_range_B_refined 5.26 r_long_range_B_other 4.906 r_scangle_other 2.705 r_scbond_it 1.765 r_scbond_other 1.764 r_mcangle_it 1.701
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.231 r_dihedral_angle_3_deg 10.402 r_dihedral_angle_4_deg 9.084 r_dihedral_angle_1_deg 6.996 r_long_range_B_refined 5.26 r_long_range_B_other 4.906 r_scangle_other 2.705 r_scbond_it 1.765 r_scbond_other 1.764 r_mcangle_it 1.701 r_mcangle_other 1.701 r_angle_refined_deg 1.201 r_mcbond_it 1.059 r_mcbond_other 1.057 r_angle_other_deg 0.624 r_chiral_restr 0.081 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 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 4581 Nucleic Acid Atoms Solvent Atoms 781 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling autoSHARP phasing