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Crystal Structure of Ad37 fiber knob in complex with GD1a oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UXE pdb entry 1uxe
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 26% PEG 8000, 0.05M zinc acetate, 0.1M HEPES, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.44 49.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.99 α = 90 b = 69.77 β = 94.92 c = 74.9 γ = 90
Symmetry Space Group P 1 21 1
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 MARMOSAIC 225 mm CCD mirrors 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.65 32.9 99.1 0.051 14.2 4.1 75294 74636 2.2 2.2 30
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 1.65 1.69 98.4 0.54 2.2 3.9 5420
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) 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 pdb entry 1uxe 1.65 32.9 2.2 74636 73139 1494 99.1 0.16 0.16 0.16 0.1924 0.187 0.2188 2.0% of reflections 27.587
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] 0.42 0.8 0.27 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_4_deg 11.403 r_dihedral_angle_1_deg 6.461 r_scangle_it 3.42 r_scbond_it 2.608 r_mcangle_it 2.413 r_mcbond_it 1.751 r_angle_refined_deg 1.502 r_angle_other_deg 1.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.818 r_dihedral_angle_3_deg 11.675 r_dihedral_angle_4_deg 11.403 r_dihedral_angle_1_deg 6.461 r_scangle_it 3.42 r_scbond_it 2.608 r_mcangle_it 2.413 r_mcbond_it 1.751 r_angle_refined_deg 1.502 r_angle_other_deg 1.091 r_mcbond_other 0.947 r_chiral_restr 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4335 Nucleic Acid Atoms Solvent Atoms 527 Heterogen Atoms 91
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction