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E. coli BamA beta-barrel bound to cyclic peptide CP3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NRE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 2.5% w/v TBPB, 0.2 M sodium formate, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 3.14 60.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.084 α = 90 b = 78.987 β = 90 c = 124.979 γ = 90
Symmetry Space Group P 2 2 21
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 2023-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0001 SLS X06SA
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 1.784 78.987 82.6 0.061 0.068 0.03 0.999 12.4 5 45901
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 1.784 1.898 24.7 0.857 1 0.505 0.511 1.4 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.784 25.98 45873 2256 82.6 0.2171 0.2156 0.212 0.2466 0.239 RANDOM 37.3
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] 0.3133 -0.3583 0.0449
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.92 t_omega_torsion 3.87 t_angle_deg 0.97 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.92 t_omega_torsion 3.87 t_angle_deg 0.97 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3188 Nucleic Acid Atoms Solvent Atoms 231 Heterogen Atoms 62
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction autoPROC data scaling DIMPLE phasing