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Structure of VinM-VinL complex
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 7.5 293 HEPES-Na, sodium citrate
Crystal Properties Matthews coefficient Solvent content 2.3 46.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.501 α = 94.18 b = 72.987 β = 90.87 c = 80.209 γ = 103.34
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 PILATUS3 S 6M 2022-05-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.3 50 97.9 0.049 0.999 11.2 3.5 54087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.37 97.3 0.626 0.826 1.6 3.4
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.3 46.04 51384 2703 97.91 0.2089 0.2067 0.2106 0.2508 0.2511 RANDOM 62.016
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] 0.94 0.57 -1.12 -0.65 -0.62 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.535 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 7.152 r_angle_other_deg 1.639 r_angle_refined_deg 1.445 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.535 r_dihedral_angle_4_deg 19.119 r_dihedral_angle_3_deg 17.3 r_dihedral_angle_1_deg 7.152 r_angle_other_deg 1.639 r_angle_refined_deg 1.445 r_chiral_restr 0.063 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8624 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction Aimless data scaling MOLREP phasing Coot model building