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Crystal structure of the Myxococcus Xanthus hemagglutinin in complex with a3,a6-mannopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FBR PDB entry 4FBR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.05 M monobasic potassium phosphate and 20% w/v polyethylene glycol 3350, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.48 50.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.592 α = 90 b = 57.319 β = 90 c = 105.969 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 93 CCD RIGAKU SATURN 944 2011-07-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
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 1.76 33.82 96.8 0.053 22.1 6.63 28299 27394 1 3.8
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 1.76 1.82 81.5 0.206 3.8 2.53 2789
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 4FBR 1.76 33.82 3.8 26858 25993 1375 96.78 0.18764 0.18764 0.18622 0.21368 0.2165 RANDOM 24.264
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] -0.37 0.91 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.364 r_dihedral_angle_3_deg 10.787 r_dihedral_angle_1_deg 6.392 r_dihedral_angle_4_deg 5.071 r_scangle_it 2.249 r_scbond_it 1.583 r_angle_refined_deg 1.4 r_mcangle_it 1.124 r_mcbond_it 0.684 r_chiral_restr 0.094
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.364 r_dihedral_angle_3_deg 10.787 r_dihedral_angle_1_deg 6.392 r_dihedral_angle_4_deg 5.071 r_scangle_it 2.249 r_scbond_it 1.583 r_angle_refined_deg 1.4 r_mcangle_it 1.124 r_mcbond_it 0.684 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1963 Nucleic Acid Atoms Solvent Atoms 197 Heterogen Atoms 128
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling