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S-layer protein SlpA from Lactobacillus amylovorus, domain I (aa 32-209), important for Self-assembly
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QLH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Protein stock solution of 15 mg/mL in 20 mM Hepes pH 8 and 100 mM NaCl;
Condition: 1.0 M Ammonium formate, 0.1 M Sodium acetate pH 5.0, 8 % w/v PGA with protein end concentration of 7.5 mg/mL corresponding to 50% of protein solution in the 1.0 uL drop
Crystal Properties Matthews coefficient Solvent content 3.24 62.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.194 α = 90 b = 43.854 β = 95.498 c = 86.384 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 PIXEL DECTRIS PILATUS 6M 2019-05-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.004700 PETRA III, DESY P11
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 3.4 42.993 99.3 0.201 0.278 0.191 0.985 5.2 3.3 7031
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 3.4 3.67 0.643 0.883 0.603 0.854 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3.401 42.993 6996 334 98.702 0.254 0.2506 0.2505 0.3306 0.3298 74.477
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] -2.589 -9.292 6.019 -1.612
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.328 r_dihedral_angle_3_deg 14.244 r_lrange_it 13.061 r_lrange_other 13.054 r_mcangle_other 9.369 r_mcangle_it 9.368 r_dihedral_angle_1_deg 8.838 r_scangle_it 8.59 r_scangle_other 8.433 r_mcbond_it 5.642
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.328 r_dihedral_angle_3_deg 14.244 r_lrange_it 13.061 r_lrange_other 13.054 r_mcangle_other 9.369 r_mcangle_it 9.368 r_dihedral_angle_1_deg 8.838 r_scangle_it 8.59 r_scangle_other 8.433 r_mcbond_it 5.642 r_mcbond_other 5.628 r_scbond_it 4.964 r_scbond_other 4.856 r_dihedral_angle_2_deg 3.164 r_angle_refined_deg 1.223 r_angle_other_deg 0.424 r_symmetry_xyhbond_nbd_refined 0.346 r_symmetry_nbd_refined 0.306 r_nbd_other 0.259 r_ncsr_local_group_1 0.207 r_nbd_refined 0.198 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.17 r_symmetry_xyhbond_nbd_other 0.102 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.057 r_gen_planes_refined 0.005 r_bond_refined_d 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2676 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement REFMAC refinement XDS data reduction pointless data scaling PHASER phasing