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Crystal structure of the OrfX1-OrfX3 complex from the PMP1 neurotoxin gene cluster
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.2 M sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.29 62.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.018 α = 90 b = 126.573 β = 90 c = 154.218 γ = 90
Symmetry Space Group P 21 21 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 EIGER X 16M 2019-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.9762 MAX IV BioMAX
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 2.7 77.1 99.9 0.14 0.16 0.06 0.99 8.5 10 50841
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 2.7 2.79 99.1 1.56 0.742 1.2 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 Alphafold model 2.7 63.367 50701 2545 99.917 0.224 0.2224 0.2207 0.2629 0.2624 53.008
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] 12.337 -4.639 -7.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.002 r_dihedral_angle_3_deg 18.307 r_dihedral_angle_4_deg 14.841 r_lrange_it 6.89 r_dihedral_angle_1_deg 6.576 r_scangle_it 4.773 r_mcangle_it 3.916 r_scbond_it 2.878 r_mcbond_it 2.42 r_angle_refined_deg 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.002 r_dihedral_angle_3_deg 18.307 r_dihedral_angle_4_deg 14.841 r_lrange_it 6.89 r_dihedral_angle_1_deg 6.576 r_scangle_it 4.773 r_mcangle_it 3.916 r_scbond_it 2.878 r_mcbond_it 2.42 r_angle_refined_deg 1.602 r_nbtor_refined 0.312 r_symmetry_xyhbond_nbd_refined 0.246 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.203 r_xyhbond_nbd_refined 0.134 r_chiral_restr 0.103 r_bond_refined_d 0.01 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9696 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing