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Structure of the lectin Bambl from Burkholderia ambifaria in complex with blood group H type 1 tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZW0 PDB ENTRY 3ZW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 3 M MALONATE PH 6.0. 10% ETHYLENE GLYCOL WAS ADDED AS CRYOPROTECTANT PRIOR FREEZING
Crystal Properties Matthews coefficient Solvent content 1.99 38.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.64 α = 90 b = 47.57 β = 103.19 c = 72.94 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 ADSC QUANTUM 315r 2010-11-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.6 39.52 95.3 0.07 7.1 2.8 29207 2 17.2
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 1.6 1.69 78.9 0.18 2.5 2.5
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 PDB ENTRY 3ZW0 1.6 39.52 27618 1456 94.74 0.16216 0.16009 0.166 0.20235 0.2045 RANDOM 14.239
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] 1.64 0.84 -0.23 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.252 r_dihedral_angle_3_deg 11.637 r_dihedral_angle_4_deg 7.531 r_dihedral_angle_1_deg 6.83 r_scangle_it 2.875 r_scbond_it 2.047 r_angle_refined_deg 1.681 r_mcangle_it 1.532 r_angle_other_deg 1.223 r_mcbond_it 0.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.252 r_dihedral_angle_3_deg 11.637 r_dihedral_angle_4_deg 7.531 r_dihedral_angle_1_deg 6.83 r_scangle_it 2.875 r_scbond_it 2.047 r_angle_refined_deg 1.681 r_mcangle_it 1.532 r_angle_other_deg 1.223 r_mcbond_it 0.904 r_mcbond_other 0.265 r_nbd_other 0.201 r_nbtor_refined 0.188 r_symmetry_vdw_other 0.188 r_nbd_refined 0.176 r_xyhbond_nbd_refined 0.172 r_symmetry_hbond_refined 0.17 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.105 r_nbtor_other 0.097 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1983 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 213
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing