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Crystal Structure of Sodium/Sugar symporter with bound Galactose from vibrio parahaemolyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 278 100 mM Hepes, 200mM Ca Acetate, 20-25% PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 4.37 71.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.28 α = 109.7 b = 109.21 β = 92.02 c = 127.58 γ = 102.11
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 ADSC QUANTUM 315 2008-02-25 M SINGLE WAVELENGTH 2 1 CCD MARMOSAIC 300 mm CCD 2008-02-17
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 0.97930 ALS 5.0.2 2 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97930 APS 23-ID-D
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 2.7 30 91.3 0.113 8.6 4 103009
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 2.7 2.8 69.9 0.429 1.55 1.7
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SIRAS THROUGHOUT 2.7 30 57175 2998 53.33 0.27063 0.26979 0.3302 0.28715 0.3399 RANDOM 37.531
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] 0.35 0.26 -0.61 0.19 0.06 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_3_deg 19.479 r_dihedral_angle_4_deg 17.133 r_dihedral_angle_1_deg 6.796 r_angle_other_deg 4.379 r_scangle_it 2.467 r_scbond_it 2.303 r_mcangle_it 1.819 r_angle_refined_deg 1.071 r_mcbond_it 0.949
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.834 r_dihedral_angle_3_deg 19.479 r_dihedral_angle_4_deg 17.133 r_dihedral_angle_1_deg 6.796 r_angle_other_deg 4.379 r_scangle_it 2.467 r_scbond_it 2.303 r_mcangle_it 1.819 r_angle_refined_deg 1.071 r_mcbond_it 0.949 r_mcbond_other 0.138 r_chiral_restr 0.061 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.004 r_bond_other_d r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15416 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 56
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction