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Crystal structure of S-layer protein SlpA from Lactobacillus acidophilus, domain I (aa 32-198)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QLD
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;
JCSG+ screen condition A5 (0.2 M Magnesium formate dihydrate, 20 % w/v PEG 3350) 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 2.22 44.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.127 α = 90 b = 39.036 β = 101.662 c = 60.058 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-F 2015-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97895 ESRF ID23-1
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 2.6 48.37 99.3 0.143 0.198 0.137 0.986 7.1 3.3 9254
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 2.6 2.72 0.574 0.794 0.547 0.666 3.4
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 7QLD 2.6 48.367 9252 462 99.111 0.203 0.2003 0.2002 0.2583 0.2585 32.184
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] 2.068 -0.156 1.597 -3.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.648 r_dihedral_angle_3_deg 15.089 r_lrange_it 8.224 r_lrange_other 8.223 r_dihedral_angle_1_deg 7.237 r_mcangle_it 4.836 r_mcangle_other 4.834 r_scangle_it 4.497 r_scangle_other 4.496 r_mcbond_it 2.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.648 r_dihedral_angle_3_deg 15.089 r_lrange_it 8.224 r_lrange_other 8.223 r_dihedral_angle_1_deg 7.237 r_mcangle_it 4.836 r_mcangle_other 4.834 r_scangle_it 4.497 r_scangle_other 4.496 r_mcbond_it 2.906 r_mcbond_other 2.902 r_scbond_it 2.708 r_scbond_other 2.706 r_angle_refined_deg 1.605 r_angle_other_deg 1.271 r_symmetry_xyhbond_nbd_refined 0.212 r_nbd_refined 0.207 r_symmetry_nbd_other 0.176 r_nbd_other 0.176 r_nbtor_refined 0.151 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.105 r_ncsr_local_group_1 0.105 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2193 Nucleic Acid Atoms Solvent Atoms 129 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building