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Crystal structure of maltodextrin-binding protein SPs0871 from Streptococcus pyogenes at 2.20 A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5MKB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.13 Ammonium citrate tribasic 1.8 M
Crystal Properties Matthews coefficient Solvent content 2.83 56.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.189 α = 90 b = 118.189 β = 90 c = 353.944 γ = 120
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 PILATUS3 S 6M 2021-03-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 45.3 98.4 0.084 0.02 0.999 21.9 17.3 47995
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.32 89.4 0.352 0.098 0.985 6.8 13.4
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 THROUGHOUT 2.2 45.3 47994 2392 98.427 0.187 0.1849 0.1932 0.2237 0.2297 40.898
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] 1.516 0.758 1.516 -4.918
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.411 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 6.434 r_lrange_it 5.558 r_lrange_other 5.541 r_scangle_it 4.467 r_scangle_other 4.467 r_dihedral_angle_2_deg 3.821 r_scbond_it 2.805 r_scbond_other 2.804
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.411 r_dihedral_angle_3_deg 14.363 r_dihedral_angle_1_deg 6.434 r_lrange_it 5.558 r_lrange_other 5.541 r_scangle_it 4.467 r_scangle_other 4.467 r_dihedral_angle_2_deg 3.821 r_scbond_it 2.805 r_scbond_other 2.804 r_mcangle_it 2.69 r_mcangle_other 2.69 r_mcbond_it 1.854 r_mcbond_other 1.852 r_angle_refined_deg 1.462 r_angle_other_deg 0.494 r_nbd_refined 0.217 r_symmetry_nbd_other 0.188 r_symmetry_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.18 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.127 r_symmetry_nbtor_other 0.078 r_ncsr_local_group_1 0.075 r_chiral_restr 0.07 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5625 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing