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WxLIP from Enterococcus faecium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 300 lithium sulfate, sodium acetate, PEG400
Crystal Properties Matthews coefficient Solvent content 2.42 49.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.54 α = 90 b = 102.719 β = 90 c = 118.795 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2023-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97622 Diamond I03
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 1.95 51.4 99.9 0.116 0.12 0.032 0.999 12.7 13.7 45950
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 1.95 5.29 100 3.623 3.759 0.994 0.255 0.4
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 THROUGHOUT 1.95 51.4 45919 2050 99.765 0.194 0.1916 0.189 0.2466 0.2462 50.189
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] 0.427 -1.274 0.847
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.872 r_dihedral_angle_6_deg 17.546 r_dihedral_angle_2_deg 15.961 r_lrange_other 11.111 r_lrange_it 11.097 r_scangle_it 9.167 r_scangle_other 9.165 r_dihedral_angle_1_deg 7.992 r_scbond_it 6.714 r_scbond_other 6.714
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.872 r_dihedral_angle_6_deg 17.546 r_dihedral_angle_2_deg 15.961 r_lrange_other 11.111 r_lrange_it 11.097 r_scangle_it 9.167 r_scangle_other 9.165 r_dihedral_angle_1_deg 7.992 r_scbond_it 6.714 r_scbond_other 6.714 r_mcangle_other 6.233 r_mcangle_it 6.227 r_mcbond_it 4.688 r_mcbond_other 4.687 r_angle_refined_deg 2.175 r_angle_other_deg 0.694 r_symmetry_nbd_refined 0.261 r_symmetry_xyhbond_nbd_refined 0.24 r_xyhbond_nbd_refined 0.221 r_nbd_refined 0.214 r_symmetry_nbd_other 0.213 r_nbtor_refined 0.188 r_nbd_other 0.178 r_symmetry_nbtor_other 0.098 r_chiral_restr 0.091 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4175 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing