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Crystal structure of the complex formed between goat signalling protein with pentasaccharide at 3.1 A resolution reveals large scale conformational changes in the residues of TIM barrel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1QZO PDB ENTRY 1QZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 298 25mM Tris HCl, 50mM NaCl, 19% ethanol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K, pH 7.80
Crystal Properties Matthews coefficient Solvent content 2.8 56.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.745 α = 90 b = 66.613 β = 90 c = 107.812 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 2005-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300
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 3.1 56.7 98.5 0.11 7 8493
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 3.1 3.21 99.5 0.43 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 1QZO 3.1 56.7 8493 8090 403 98.17 0.17859 0.1766 0.21782 RANDOM 24.973
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] 0.4 0.08 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.793 r_scangle_it 5.634 r_scbond_it 3.417 r_mcangle_it 3.163 r_angle_refined_deg 2.44 r_angle_other_deg 2.381 r_dihedral_angle_1_deg 2.243 r_mcbond_it 1.683 r_nbtor_other 0.472 r_symmetry_vdw_other 0.409
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 22.793 r_scangle_it 5.634 r_scbond_it 3.417 r_mcangle_it 3.163 r_angle_refined_deg 2.44 r_angle_other_deg 2.381 r_dihedral_angle_1_deg 2.243 r_mcbond_it 1.683 r_nbtor_other 0.472 r_symmetry_vdw_other 0.409 r_symmetry_vdw_refined 0.311 r_nbd_refined 0.296 r_nbd_other 0.268 r_symmetry_hbond_refined 0.258 r_xyhbond_nbd_refined 0.233 r_xyhbond_nbd_other 0.231 r_chiral_restr 0.152 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_4_deg r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2876 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 98
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing