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Crystal structure of the N-terminal domain (residues 1-137) of MPXV A7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8IZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M Potassium thiocyanate, 30% w/v Polyethylene glycol monomethyl ether 2000
Crystal Properties Matthews coefficient Solvent content 3.16 61.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.903 α = 90 b = 140.327 β = 90 c = 153.519 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 2022-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97851 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.54 19.45 99.8 0.997 14.1 12.8 14013
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.54 2.65 0.954
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 (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 8IZT 2.54 19.45 13250 677 99.26 0.20288 0.20106 0.2104 0.23776 0.2387 RANDOM 69.853
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] 8.66 -1.36 -7.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.816 r_dihedral_angle_4_deg 19.868 r_dihedral_angle_3_deg 16.998 r_long_range_B_other 13.108 r_long_range_B_refined 13.105 r_scangle_other 10.577 r_mcangle_other 9.907 r_mcangle_it 9.901 r_mcbond_it 6.929 r_scbond_it 6.908
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.816 r_dihedral_angle_4_deg 19.868 r_dihedral_angle_3_deg 16.998 r_long_range_B_other 13.108 r_long_range_B_refined 13.105 r_scangle_other 10.577 r_mcangle_other 9.907 r_mcangle_it 9.901 r_mcbond_it 6.929 r_scbond_it 6.908 r_mcbond_other 6.89 r_scbond_other 6.856 r_dihedral_angle_1_deg 6.033 r_angle_refined_deg 1.578 r_angle_other_deg 1.309 r_chiral_restr 0.071 r_bond_refined_d 0.008 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 2206 Nucleic Acid Atoms Solvent Atoms 87 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing