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Crystal structure of self-complemented PsaA, the major subunit of pH 6 antigen from Yersinia pests, in complex with choline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LND
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.8 294 0.1 M imidazole, 0.2 M zinc acetate and 18% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.56 65.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.542 α = 90 b = 44.625 β = 120.36 c = 99.441 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 PIXEL DECTRIS PILATUS3 6M 2012-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.36 49.4 99.5 0.082 11.2 3.5 25917
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 2.36 2.44 99.6 0.63 1.2 3.5
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 5LND 2.36 49.397 24595 1322 99.41 0.2314 0.2294 0.2298 0.2685 0.2665 RANDOM 44.315
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] 1.7 1.48 -2.36 -0.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 18.439 r_dihedral_angle_4_deg 9.292 r_dihedral_angle_1_deg 8.112 r_mcangle_it 5.489 r_scbond_it 4.667 r_mcbond_it 3.671 r_angle_refined_deg 2.256 r_chiral_restr 0.129 r_bond_refined_d 0.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.844 r_dihedral_angle_3_deg 18.439 r_dihedral_angle_4_deg 9.292 r_dihedral_angle_1_deg 8.112 r_mcangle_it 5.489 r_scbond_it 4.667 r_mcbond_it 3.671 r_angle_refined_deg 2.256 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3116 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 21
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction