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Lol B - Localization of lipoprotein B from Vibrio cholera
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IWM Crystal Structure of the Outer Membrane Lipoprotein Receptor, LolB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 291.15 0.1M KCl, 0.1 M Bis-Tris 6.0, 18% w/v PEG4000
Crystal Properties Matthews coefficient Solvent content 2.55 51.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.414 α = 90 b = 113.414 β = 90 c = 34.15 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 16M 2020-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.97624 MAX IV BioMAX
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.46 40.1 100 0.127 0.132 0.026 0.999 19.6 2 39405
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.46 1.512 99.97 0.3738 0.5287 0.3738 0.752 1.69
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.46 35.86 1.34 39342 1932 99.99 0.1673 0.1658 0.1652 0.1972 0.1966 24.12
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 5.8729 f_angle_d 0.9546 f_chiral_restr 0.0885 f_plane_restr 0.0067 f_bond_d 0.0064
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1486 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction autoPROC data scaling PHENIX phasing