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Lexapeptide dehydratase complex LxmKY, ATP bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Previously solved LxmKY apo structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 291.15 0.1 M Bis-Tris propane 7.5 20 % w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.22 61.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.716 α = 90 b = 120.661 β = 90 c = 152.767 γ = 90
Symmetry Space Group P 2 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 2022-03-13 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 2.5 49.282 100 0.221 0.239 0.089 0.99 7.2 13.4 37827
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 2.5 2.6 100 4.278 4.619 1.735 0.623 1.1
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 2.5 49.282 37783 1916 99.947 0.227 0.2243 0.2271 0.2676 0.273 70.592
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] -3.765 4.385 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.932 r_dihedral_angle_3_deg 15.422 r_dihedral_angle_2_deg 13.782 r_lrange_other 12.081 r_lrange_it 12.079 r_mcangle_it 9.238 r_mcangle_other 9.237 r_scangle_it 9.115 r_scangle_other 9.114 r_mcbond_it 6.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.932 r_dihedral_angle_3_deg 15.422 r_dihedral_angle_2_deg 13.782 r_lrange_other 12.081 r_lrange_it 12.079 r_mcangle_it 9.238 r_mcangle_other 9.237 r_scangle_it 9.115 r_scangle_other 9.114 r_mcbond_it 6.27 r_mcbond_other 6.261 r_scbond_it 6.226 r_scbond_other 6.224 r_dihedral_angle_1_deg 6.092 r_chiral_restr_other 1.537 r_angle_refined_deg 1.378 r_angle_other_deg 0.813 r_nbd_other 0.257 r_symmetry_nbd_other 0.231 r_nbd_refined 0.228 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.163 r_symmetry_nbd_refined 0.161 r_symmetry_xyhbond_nbd_other 0.114 r_symmetry_xyhbond_nbd_refined 0.085 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.06 r_bond_refined_d 0.014 r_gen_planes_other 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4757 Nucleic Acid Atoms Solvent Atoms 71 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing