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Phage Phi106 repressor in complex with AimX
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 294 20% PEG 3350, 100mM Zinc Acetate, 100mM imidazole pH8
Crystal Properties Matthews coefficient Solvent content 2.25 45.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.991 α = 90 b = 56.991 β = 90 c = 100.716 γ = 90
Symmetry Space Group P 43 21 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 PILATUS 6M 2025-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.97926 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.7 49.601 100 0.012 35.1 25 19015
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.79 100 0.077 9.1 26.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.7 49.601 18942 976 99.937 0.181 0.1787 0.2187 0.2373 42.297
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] -0.58 -0.58 1.16
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.076 r_lrange_other 24.07 r_scangle_it 19.06 r_scangle_other 19.05 r_dihedral_angle_6_deg 17.148 r_mcangle_it 15.425 r_mcangle_other 15.419 r_scbond_it 14.386 r_scbond_other 14.376 r_dihedral_angle_3_deg 14.208
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 24.076 r_lrange_other 24.07 r_scangle_it 19.06 r_scangle_other 19.05 r_dihedral_angle_6_deg 17.148 r_mcangle_it 15.425 r_mcangle_other 15.419 r_scbond_it 14.386 r_scbond_other 14.376 r_dihedral_angle_3_deg 14.208 r_mcbond_it 11.669 r_mcbond_other 11.353 r_dihedral_angle_2_deg 6.201 r_rigid_bond_restr 5.893 r_dihedral_angle_1_deg 5.079 r_angle_refined_deg 1.724 r_angle_other_deg 0.785 r_nbd_refined 0.212 r_symmetry_nbd_refined 0.196 r_nbd_other 0.195 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.164 r_symmetry_nbd_other 0.152 r_symmetry_xyhbond_nbd_refined 0.125 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.065 r_symmetry_metal_ion_refined 0.062 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1220 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 39
Software Software Software Name Purpose SCALA data scaling gemmi data extraction REFMAC refinement XDS data reduction MOLREP phasing