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Crystal structure of the Periplasmic Sialic Acid Binding Protein from Vibrio Cholerea
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B50 PDB ENTRY 3B50
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 277 36 mg/ml SiaP in 20 mM HEPES, 10 mM sodium chloride, pH 8.0 and reservoir solution (0.1 M MES, 20% w/v PEG-6000 at pH 6.0). , VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.977 α = 90 b = 82.315 β = 90 c = 119.354 γ = 90
Symmetry Space Group I 2 2 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 MAR CCD 165 mm 2006-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.9793 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 19.91 99.8 0.073 7.9 6.04 65540 65409 24.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.5 100 0.655 1.8 5.97 6477
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-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3B50 1.45 11.73 65331 3314 99.82 0.184 0.184 0.1822 0.1939 0.2194 0.2245 RANDOM 29.4153
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] -0.34 -0.45 0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.568 r_dihedral_angle_4_deg 14.508 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 4.906 r_scangle_it 3.595 r_scbond_it 2.484 r_mcangle_it 1.49 r_mcbond_it 1.267 r_angle_refined_deg 1.233 r_angle_other_deg 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.568 r_dihedral_angle_4_deg 14.508 r_dihedral_angle_3_deg 11.603 r_dihedral_angle_1_deg 4.906 r_scangle_it 3.595 r_scbond_it 2.484 r_mcangle_it 1.49 r_mcbond_it 1.267 r_angle_refined_deg 1.233 r_angle_other_deg 0.896 r_mcbond_other 0.373 r_symmetry_vdw_refined 0.234 r_symmetry_vdw_other 0.222 r_nbd_refined 0.21 r_nbd_other 0.185 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.153 r_symmetry_hbond_refined 0.151 r_nbtor_other 0.086 r_chiral_restr 0.076 r_xyhbond_nbd_other 0.025 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2445 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 6
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection AMoRE phasing