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Lexapeptide dehydratase complex LxmKY apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold AF-A6THA0-F1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 291.15 0.2 M sodium acetate trihydrate; 0.1 M Bis-Tris propane pH 7.5; 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.16 42.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.704 α = 90 b = 90.28 β = 90 c = 148.953 γ = 90
Symmetry Space Group P 21 21 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 2022-07-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.954 Australian Synchrotron MX2
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 2.4 48.62 100 0.434 0.45 0.118 0.996 8.6 27.3 31270
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 2.4 2.49 2.794 3.152 1.433 0.369 4.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION SAD FREE R-VALUE 2.4 48.62 31211 1613 99.984 0.214 0.2114 0.2148 0.2654 0.2663 50.996
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] 0.368 1.13 -1.498
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.384 r_dihedral_angle_6_deg 16.207 r_dihedral_angle_2_deg 15.043 r_lrange_it 10.242 r_lrange_other 10.238 r_scangle_it 8.282 r_scangle_other 8.281 r_mcangle_it 7.29 r_mcangle_other 7.289 r_scbond_it 5.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.384 r_dihedral_angle_6_deg 16.207 r_dihedral_angle_2_deg 15.043 r_lrange_it 10.242 r_lrange_other 10.238 r_scangle_it 8.282 r_scangle_other 8.281 r_mcangle_it 7.29 r_mcangle_other 7.289 r_scbond_it 5.842 r_scbond_other 5.84 r_dihedral_angle_1_deg 5.627 r_mcbond_it 5.072 r_mcbond_other 5.058 r_chiral_restr_other 1.537 r_angle_refined_deg 1.496 r_angle_other_deg 0.902 r_symmetry_xyhbond_nbd_refined 0.457 r_symmetry_nbd_refined 0.255 r_symmetry_nbd_other 0.236 r_nbd_refined 0.212 r_nbd_other 0.201 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.164 r_metal_ion_refined 0.13 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.063 r_symmetry_xyhbond_nbd_other 0.024 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_gen_planes_other 0.006 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4796 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing