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CRYSTAL STRUCTURE OF A BUFFALO SIGNALING GLYCOPROTEIN (SPB-40) SECRETED DURING INVOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LJY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICRODIALYSIS 8 298 16% ETHANOL, 25MM TRIS, pH 8.0, MICRODIALYSIS, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.764 α = 90 b = 66.559 β = 90 c = 107.137 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 295 IMAGE PLATE MARRESEARCH 1999-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5417
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 2.9 20 75.5 0.171 11 8070
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 2.9 2.95 0.342 2.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LJY 2.9 20 8070 318 100 0.23987 0.23747 0.28806 RANDOM 41.247
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] -2.26 -2.03 4.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.879 r_angle_refined_deg 1.928 r_symmetry_hbond_refined 0.45 r_nbd_refined 0.304 r_symmetry_vdw_refined 0.261 r_xyhbond_nbd_refined 0.249 r_chiral_restr 0.134 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 3.879 r_angle_refined_deg 1.928 r_symmetry_hbond_refined 0.45 r_nbd_refined 0.304 r_symmetry_vdw_refined 0.261 r_xyhbond_nbd_refined 0.249 r_chiral_restr 0.134 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2894 Nucleic Acid Atoms Solvent Atoms 64 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing