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Crystal structure of a coronaviral M protein in complex with a C-terminal peptide of the N protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7Y9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIPIDIC CUBIC PHASE 8.8 293.15 300 mM ammonium formate, 50 mM Tris-HCl pH 8.8, 35% PEG 500 MME, 7.1 mM pentaethylene glycol monooctyl ether, soaked with 1 mM VPSFEDVVDA peptide
Crystal Properties Matthews coefficient Solvent content 3.02 59.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.544 α = 90 b = 220.132 β = 90 c = 71.097 γ = 90
Symmetry Space Group C 2 2 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 PILATUS 6M 2024-05-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.97946 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 3.025 20.151 86 0.165 0.185 0.081 7.2 4.8 10543
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.025 3.127 45.8 1.283 1.407 0.57 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.142 20.106 1.35 10332 486 94.25 0.2563 0.2545 0.2587 0.2909 0.2879
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.844 f_angle_d 0.474 f_chiral_restr 0.042 f_plane_restr 0.004 f_bond_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3095 Nucleic Acid Atoms Solvent Atoms 16 Heterogen Atoms 48
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing