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Crystal structure of the complex of signaling glycoprotein from buffalo (SPB-40) with tetrahydropyran at 2.5 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O9O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 25mM Tris, 50mM NaCl, 20% ethanol, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.67 53.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.174 α = 90 b = 67.088 β = 90 c = 106.569 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 77 CCD MARRESEARCH MIRROR 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.5 50 95.7 0.102 19.1 15750 15750
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.47 2.5 97.7 0.478 3.1
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 (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 2O9O 2.5 41.76 14157 756 94.6 0.24741 0.24656 0.2466 0.26329 0.2618 RANDOM 33.741
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] -2.53 -2.59 5.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 26.003 r_dihedral_angle_3_deg 23.163 r_long_range_B_refined 7.902 r_long_range_B_other 7.9 r_dihedral_angle_1_deg 7.093 r_scangle_other 4.814 r_mcangle_other 4.478 r_mcangle_it 4.477 r_scbond_it 3.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.928 r_dihedral_angle_4_deg 26.003 r_dihedral_angle_3_deg 23.163 r_long_range_B_refined 7.902 r_long_range_B_other 7.9 r_dihedral_angle_1_deg 7.093 r_scangle_other 4.814 r_mcangle_other 4.478 r_mcangle_it 4.477 r_scbond_it 3.027 r_scbond_other 3.026 r_mcbond_it 2.776 r_mcbond_other 2.771 r_angle_refined_deg 1.785 r_angle_other_deg 0.924 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 20
Software Software Software Name Purpose HKL-2000 data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling