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Crystal structure of the trimeric autotransporter adhesin head domain BpaA from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LA9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 JCSG+ C12, 10% PEG 1000, 10% PEG 8000, crystal tracking ID 203139c12, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.74 29.485
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.718 α = 90 b = 50.718 β = 90 c = 136.496 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 100 CCD ADSC QUANTUM 315r 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 1.5418 ALS 5.0.3
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 1.35 50 98.9 0.075 16.5 4.9 28462
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) 1.35 1.37 81.7 0.399 2.14 2.7 1196
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 3LA9 1.35 45.5 28461 1437 98.88 0.115 0.114 0.1195 0.128 0.1341 RANDOM 16.331
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] 1.86 1.86 -3.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_dihedral_angle_4_deg 32.563 r_dihedral_angle_3_deg 9.582 r_dihedral_angle_1_deg 5.42 r_scangle_it 2.749 r_scbond_it 1.898 r_mcangle_it 1.271 r_angle_refined_deg 1.116 r_mcbond_it 0.778 r_rigid_bond_restr 0.736
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.785 r_dihedral_angle_4_deg 32.563 r_dihedral_angle_3_deg 9.582 r_dihedral_angle_1_deg 5.42 r_scangle_it 2.749 r_scbond_it 1.898 r_mcangle_it 1.271 r_angle_refined_deg 1.116 r_mcbond_it 0.778 r_rigid_bond_restr 0.736 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1136 Nucleic Acid Atoms Solvent Atoms 184 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling