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Near-atomic resolution analysis of BipD- A component of the type-III secretion system of Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IZP PDB ENTRY 2IZP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 298 35% PEG 4000, 0.1M glycine, 0.02M EDTA, 0.06M cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.1 41.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.15 α = 90 b = 60.42 β = 96.01 c = 90.415 γ = 90
Symmetry Space Group C 1 2 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 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.9763 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.5 34.71 98.3 0.067 0.067 13.7 5.1 42898 16.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.5 1.6 99.4 0.556 0.556 2 3.5 6210
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 (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 2IZP 1.51 34.71 40761 2157 99.73 0.161 0.161 0.161 0.169 0.198 0.201 RANDOM 16.3
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] -0.18 -0.12 0.41 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.049 r_dihedral_angle_4_deg 19.694 r_dihedral_angle_3_deg 13.439 r_sphericity_free 6.853 r_sphericity_bonded 6.258 r_scangle_it 5.055 r_dihedral_angle_1_deg 4.374 r_scbond_it 3.218 r_mcangle_it 2.467 r_rigid_bond_restr 1.544
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.049 r_dihedral_angle_4_deg 19.694 r_dihedral_angle_3_deg 13.439 r_sphericity_free 6.853 r_sphericity_bonded 6.258 r_scangle_it 5.055 r_dihedral_angle_1_deg 4.374 r_scbond_it 3.218 r_mcangle_it 2.467 r_rigid_bond_restr 1.544 r_mcbond_it 1.45 r_angle_other_deg 1.444 r_angle_refined_deg 1.269 r_mcbond_other 0.739 r_chiral_restr 0.077 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_gen_planes_other 0.001 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2025 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms
Software Software Software Name Purpose ADSC data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling