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Crystal structure of surface glycan-binding protein PbSGBP-B from Prevotella bryantii
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 50 mM MES pH 6.5, 0.2 M ammonium sulfate, 30 % PEG 5K MME, 1% (w/v) MPD, 15 mg/mL protein
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.9 α = 90 b = 82.9 β = 90 c = 152.47 γ = 90
Symmetry Space Group P 41 21 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 RAYONIX MX-300 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.19 43.33 99.7 0.082 0.032 0.999 20.2 14.3 28099
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 2.19 2.25 99.7 1.575 0.601 0.762 2.2 14.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE 2.19 43.329 1.34 28041 1377 99.68 0.2062 0.2044 0.2074 0.2401 0.2417 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 17.63 f_angle_d 0.647 f_chiral_restr 0.049 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3319 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 31
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing PHENIX model building Coot model building