☰ Navigation Tabs
Racemic protein crystal structure of lacticin Q from Lactococcus lactis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other Ideal helix fragments
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 A racemic mixture of L-lacticin Q and D-lacticin Q at 27 mg/mL concentration was mixed 1:1 with 4.0M sodium formate precipitant condition pH 7.0 in a 1 microlitre sitting drop. Crystals were submerged in 2.0M Lithium sulfate cryoprotectant and flash frozen in liquid nitrogen during harvesting.
Crystal Properties Matthews coefficient Solvent content 1.81 31.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 24.21 α = 95.03 b = 27.83 β = 90.43 c = 70.45 γ = 115.41
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 EIGER2 XE 16M 2020-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.8156 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 0.96 35.05 93 0.999 11.3 3.5 93924
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.96 0.98 84.2 0.67 1
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 Ideal helix fragments 0.96 35.05 93922 4686 92.978 0.183 0.1823 0.1864 0.2053 0.2101 13.581
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] -0.28 0.374 -0.818 -0.053 -0.852 0.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.702 r_dihedral_angle_3_deg 13.061 r_rigid_bond_restr 5.436 r_dihedral_angle_1_deg 3.923 r_lrange_it 2.616 r_lrange_other 2.546 r_scangle_it 2.54 r_scangle_other 2.54 r_scbond_it 2.255 r_scbond_other 2.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 51.702 r_dihedral_angle_3_deg 13.061 r_rigid_bond_restr 5.436 r_dihedral_angle_1_deg 3.923 r_lrange_it 2.616 r_lrange_other 2.546 r_scangle_it 2.54 r_scangle_other 2.54 r_scbond_it 2.255 r_scbond_other 2.252 r_angle_refined_deg 1.817 r_mcangle_other 1.733 r_mcangle_it 1.732 r_mcbond_other 1.357 r_mcbond_it 1.356 r_angle_other_deg 1.319 r_nbd_other 0.35 r_symmetry_nbd_refined 0.312 r_nbd_refined 0.244 r_symmetry_xyhbond_nbd_refined 0.235 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.199 r_xyhbond_nbd_refined 0.168 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.073 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1672 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling Fragon phasing Coot model building SHELXE model building XDS data reduction xia2 data reduction