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The Crystal Structure of YejA - an ABC Peptide Transporter Receptor
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ONY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291 Protein: 20 mg.ml-1 in 20 mM Tris-HCl, 50 mM NaCl, pH 8.0
Reservoir solution: 2% w/v polyethylene glycol 20,000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, pH 6.5
Drops: 300 nl (150 nl protein solution + 150 nl reservoir solution)
Reservoir: 100 microlitres
Crystal Properties Matthews coefficient Solvent content 2.57 52.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.44 α = 90 b = 105.267 β = 90 c = 145.387 γ = 90
Symmetry Space Group I 2 2 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 PILATUS3 S 6M 2017-05-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92819 Diamond I04
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 1.55 85.264 99.6 0.07 0.08 0.038 0.997 14.1 8.4 101011 15.46
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 1.55 1.58 0.668 0.756 0.353 0.904 2.4 8.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4ONY 1.55 85.264 101009 4874 99.528 0.171 0.1701 0.1686 0.1846 0.1829 20.793
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] 1.846 -0.539 -1.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 6.791 r_lrange_it 5.839 r_lrange_other 5.749 r_scangle_it 4.862 r_scangle_other 4.862 r_scbond_it 3.283 r_scbond_other 3.282
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.24 r_dihedral_angle_4_deg 17.618 r_dihedral_angle_3_deg 12.952 r_dihedral_angle_1_deg 6.791 r_lrange_it 5.839 r_lrange_other 5.749 r_scangle_it 4.862 r_scangle_other 4.862 r_scbond_it 3.283 r_scbond_other 3.282 r_mcangle_it 2.639 r_mcangle_other 2.638 r_mcbond_it 1.863 r_mcbond_other 1.839 r_angle_refined_deg 1.827 r_angle_other_deg 1.455 r_symmetry_xyhbond_nbd_refined 0.632 r_nbd_other 0.283 r_nbd_refined 0.203 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_other 0.149 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4841 Nucleic Acid Atoms Solvent Atoms 408 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement xia2 data processing Aimless data reduction Aimless data scaling MOLREP phasing