☰ Navigation Tabs
1.70 Angstrom resolution crystal structure of outer-membrane lipoprotein carrier protein (lolA) from Yersinia pestis CO92
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3KSN PDB entry 3KSN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 PEG 3350 20% w/v NH4 dihydrogen Phosphate 0.2M, protein at 34 mg/mL, cryo- 20% glycerol+paratone, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.09 41.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.201 α = 94.3 b = 67.13 β = 94.01 c = 132.563 γ = 120.01
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 MARMOSAIC 300 mm CCD Be-Lenses 2013-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 1.7 30 94.8 0.091 14.22 4.1 207123 207123 -3 23.3
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 1.7 1.73 95.4 0.598 2.7 4.1 10516
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB entry 3KSN 1.7 29.09 196543 196543 10490 93.77 0.20539 0.20355 0.2101 0.23956 0.2398 RANDOM 22.516
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] -12.08 -0.36 0.27 -10.36 -0.37 22.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.931 r_dihedral_angle_4_deg 11.736 r_dihedral_angle_3_deg 8.712 r_scangle_it 4.335 r_scbond_it 2.995 r_dihedral_angle_1_deg 2.637 r_mcangle_it 1.863 r_angle_refined_deg 1.657 r_mcbond_it 1.173 r_angle_other_deg 0.841
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.931 r_dihedral_angle_4_deg 11.736 r_dihedral_angle_3_deg 8.712 r_scangle_it 4.335 r_scbond_it 2.995 r_dihedral_angle_1_deg 2.637 r_mcangle_it 1.863 r_angle_refined_deg 1.657 r_mcbond_it 1.173 r_angle_other_deg 0.841 r_mcbond_other 0.405 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16593 Nucleic Acid Atoms Solvent Atoms 1497 Heterogen Atoms 61
Software Software Software Name Purpose Blu-Ice data collection BALBES phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling