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Crystal structure of the complex of Buffalo Secretory Glycoprotein with tetrasaccharide at 2.8A 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 7.8 298 TRIS-HCL, NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.87 α = 90 b = 66.499 β = 90 c = 107.126 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 298 IMAGE PLATE MARRESEARCH Mirror 2007-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.8 56.8 5 0.143 4.97 4.65 11568 10690 50.1
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 2.8 2.9 0.143 4.97 4.65
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 2O9O 2.8 56.8 10179 508 92.41 0.18885 0.18885 0.18693 0.1951 0.22697 0.2252 RANDOM 30.902
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] -0.87 -0.3 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.635 r_scangle_it 5.747 r_dihedral_angle_1_deg 3.656 r_scbond_it 3.497 r_angle_refined_deg 2.563 r_mcangle_it 2.399 r_mcbond_it 1.277 r_nbd_refined 0.281 r_symmetry_vdw_refined 0.277 r_xyhbond_nbd_refined 0.262
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.635 r_scangle_it 5.747 r_dihedral_angle_1_deg 3.656 r_scbond_it 3.497 r_angle_refined_deg 2.563 r_mcangle_it 2.399 r_mcbond_it 1.277 r_nbd_refined 0.281 r_symmetry_vdw_refined 0.277 r_xyhbond_nbd_refined 0.262 r_symmetry_hbond_refined 0.225 r_chiral_restr 0.194 r_bond_refined_d 0.025 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling AMoRE phasing