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Crystal structure of E.coli BamA beta-barrel in complex with nanobody B12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4N75
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 32% PEG 400, 0.2 M ammonium phosphate, 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 4.5
Crystal Properties Matthews coefficient Solvent content 4.37 71.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.709 α = 90 b = 86.664 β = 105.26 c = 125.027 γ = 90
Symmetry Space Group P 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 EIGER X 16M 2018-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.509 48.484 98.5 0.073 0.051 0.998 11.9 5.8 69491
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.51 2.57 86.3 0.973 0.699 0.621 1.2 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 4n75 2.509 48.484 1.33 69491 3566 98.38 0.2235 0.2224 0.2277 0.2442 0.2477
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 14.792 f_angle_d 0.591 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7729 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 107
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling MOLREP phasing