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E.coli YihX Wild Type Apo
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B0C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 20-60 mg/mL YihX protein in the buffer of Tris-HCl 25 mM pH 7.5, NaCl 150 mM, MgCl2 20 mM, NaF 30 mM, was mixed 1:1 ratio with the precipitant containing MES 55.5 mM, imidazole 44.5 mM pH 6.5, 30 mM MgCl2, 30 mM CaCl2, 20% glycerol, 10% PEG4000, 20% PEG500
Crystal Properties Matthews coefficient Solvent content 4.16 70.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.216 α = 90 b = 79.567 β = 90 c = 148.188 γ = 90
Symmetry Space Group I 2 2 2
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 2022-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.9 70.2 100 0.998 12.9 13.6 31737
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 1.9 1.94 0.837
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 1.9 70.2 31733 1549 99.987 0.205 0.2037 0.2123 0.2339 0.2408 42.98
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] -2.854 -4.725 7.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.829 r_dihedral_angle_3_deg 14.2 r_lrange_it 9.32 r_lrange_other 9.207 r_dihedral_angle_2_deg 8.88 r_scangle_it 7.346 r_scangle_other 7.343 r_dihedral_angle_1_deg 6.904 r_mcangle_other 5.597 r_mcangle_it 5.582
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.829 r_dihedral_angle_3_deg 14.2 r_lrange_it 9.32 r_lrange_other 9.207 r_dihedral_angle_2_deg 8.88 r_scangle_it 7.346 r_scangle_other 7.343 r_dihedral_angle_1_deg 6.904 r_mcangle_other 5.597 r_mcangle_it 5.582 r_scbond_it 5.368 r_scbond_other 5.364 r_mcbond_other 4.108 r_mcbond_it 4.103 r_angle_refined_deg 1.491 r_angle_other_deg 0.521 r_symmetry_nbd_refined 0.425 r_nbd_other 0.307 r_nbd_refined 0.228 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.188 r_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.138 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1604 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing