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Crystal structure of the Myxococcus Xanthus hemagglutinin (MBHA)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3S5V PDB entry 3S5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 0.2 M ammonium sulphate, 0.1 M sodium cacodylate trihydrate (pH 6.5) and 30% polyethylene glycol 8000, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.25 45.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.099 α = 90 b = 76.099 β = 90 c = 37.667 γ = 120
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 2011-06-11 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 1.6 32.95 97 0.094 13.2 6.48 32197 31241 1 2.2
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 1.66 88.8 0.406 2.2 3.65 2993
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 MIR THROUGHOUT PDB entry 3S5V 1.6 32.95 2.2 28963 28106 3126 97.04 0.18137 0.18137 0.17794 0.1871 0.21172 0.217 RANDOM 29.851
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] -0.43 -0.21 -0.43 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.851 r_dihedral_angle_4_deg 12.033 r_dihedral_angle_3_deg 11.994 r_dihedral_angle_1_deg 6.234 r_scangle_it 2.249 r_scbond_it 1.561 r_angle_refined_deg 1.396 r_mcangle_it 1.244 r_mcbond_it 0.76 r_chiral_restr 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.851 r_dihedral_angle_4_deg 12.033 r_dihedral_angle_3_deg 11.994 r_dihedral_angle_1_deg 6.234 r_scangle_it 2.249 r_scbond_it 1.561 r_angle_refined_deg 1.396 r_mcangle_it 1.244 r_mcbond_it 0.76 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1963 Nucleic Acid Atoms Solvent Atoms 243 Heterogen Atoms
Software Software Software Name Purpose StructureStudio data collection PHASER phasing REFMAC refinement d*TREK data reduction d*TREK data scaling