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Lexapeptide dehydratase complex LxmKY, hydrolysed ATP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously determined LxmKY apo structure
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 7.5 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.175 α = 90 b = 91.583 β = 90 c = 151.372 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 2.3 49.11 100 0.458 0.475 0.125 0.996 8.8 27.3 36800
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 2.3 2.38 100 0.41 28.2
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 MOLECULAR REPLACEMENT FREE R-VALUE 2.3 46.753 36734 1804 99.978 0.211 0.2083 0.2121 0.2571 0.2559 61.266
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] -0.657 2.016 -1.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.073 r_dihedral_angle_3_deg 15.78 r_dihedral_angle_2_deg 13.092 r_lrange_other 12.024 r_lrange_it 12.023 r_scangle_it 9.66 r_scangle_other 9.588 r_mcangle_it 8.852 r_mcangle_other 8.852 r_scbond_it 6.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.073 r_dihedral_angle_3_deg 15.78 r_dihedral_angle_2_deg 13.092 r_lrange_other 12.024 r_lrange_it 12.023 r_scangle_it 9.66 r_scangle_other 9.588 r_mcangle_it 8.852 r_mcangle_other 8.852 r_scbond_it 6.957 r_scbond_other 6.906 r_dihedral_angle_1_deg 6.316 r_mcbond_it 6.309 r_mcbond_other 6.278 r_angle_refined_deg 1.548 r_angle_other_deg 0.808 r_symmetry_xyhbond_nbd_refined 0.367 r_symmetry_nbd_other 0.23 r_nbd_other 0.229 r_nbd_refined 0.218 r_symmetry_nbd_refined 0.184 r_nbtor_refined 0.175 r_xyhbond_nbd_refined 0.148 r_xyhbond_nbd_other 0.093 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_bond_refined_d 0.011 r_gen_planes_other 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4802 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing