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WxLIP from Enterococcus faecium locus A bound to long WxL
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 7 300 sodium HEPES, PEG12000
Crystal Properties Matthews coefficient Solvent content 1.95 36.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.147 α = 90 b = 105.147 β = 90 c = 67.172 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 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 1.91 54 100 0.251 0.257 0.056 0.998 8.1 21.1 32902
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 1.91 5.18 100 5.74 5.878 1.259 0.332 0.3 21.7
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 1.911 54 32871 1687 99.945 0.219 0.2172 0.2146 0.2609 0.2578 46.435
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] 0.082 0.041 0.082 -0.265
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.252 r_dihedral_angle_3_deg 17.067 r_dihedral_angle_2_deg 11.734 r_lrange_other 9.407 r_lrange_it 9.397 r_dihedral_angle_1_deg 9.276 r_scangle_it 6.961 r_scangle_other 6.959 r_mcangle_it 5.472 r_mcangle_other 5.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.252 r_dihedral_angle_3_deg 17.067 r_dihedral_angle_2_deg 11.734 r_lrange_other 9.407 r_lrange_it 9.397 r_dihedral_angle_1_deg 9.276 r_scangle_it 6.961 r_scangle_other 6.959 r_mcangle_it 5.472 r_mcangle_other 5.47 r_scbond_it 4.72 r_scbond_other 4.718 r_mcbond_it 3.772 r_mcbond_other 3.769 r_angle_refined_deg 2.312 r_angle_other_deg 0.762 r_symmetry_xyhbond_nbd_refined 0.232 r_xyhbond_nbd_refined 0.229 r_symmetry_nbd_other 0.211 r_nbd_refined 0.209 r_nbd_other 0.207 r_nbtor_refined 0.18 r_symmetry_nbd_refined 0.148 r_chiral_restr 0.113 r_symmetry_nbtor_other 0.1 r_symmetry_xyhbond_nbd_other 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2068 Nucleic Acid Atoms Solvent Atoms 106 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing