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Crystal structure of MV in complex with LLP
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 298 0.2 M lithium sulfate,0.1 M Tris 8.5,1.26 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.66 53.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.95 α = 90 b = 112.85 β = 112.37 c = 92.244 γ = 90
Symmetry Space Group P 1 21 1
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 2M 2022-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 1.0 BESSY 14.1
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 2.27 50 95 0.122 0.136 0.059 0.991 11.3 5.4 66664
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 2.27 2.35 97.9 0.455 0.509 0.224 0.909 5
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 2.27 39.93 63136 3335 94.11 0.19283 0.18987 0.1967 0.24828 0.2517 RANDOM 19.411
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.065 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_1_deg 7.399 r_long_range_B_refined 4.617 r_long_range_B_other 4.34 r_scangle_other 2.827 r_mcangle_it 2.09 r_mcangle_other 2.09 r_scbond_it 1.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.065 r_dihedral_angle_4_deg 18.589 r_dihedral_angle_3_deg 15.58 r_dihedral_angle_1_deg 7.399 r_long_range_B_refined 4.617 r_long_range_B_other 4.34 r_scangle_other 2.827 r_mcangle_it 2.09 r_mcangle_other 2.09 r_scbond_it 1.746 r_scbond_other 1.746 r_angle_refined_deg 1.582 r_mcbond_it 1.353 r_mcbond_other 1.352 r_angle_other_deg 1.252 r_chiral_restr 0.067 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9925 Nucleic Acid Atoms Solvent Atoms 1156 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction Aimless data scaling PHASER phasing XDS data reduction