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Crystal structure of MPXV P1 protein S87P mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8XY1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 14.4% w/v PEG 8000, 80 mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 160 mM Calcium acetate, 20% v/v Glycerol
Crystal Properties Matthews coefficient Solvent content 2.35 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.366 α = 90 b = 155.5 β = 90 c = 131.736 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 2023-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97861 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 2.24 43.91 99.9 0.999 11.1 6.5 29804
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 2.24 2.31 0.949
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 8XY1 2.24 42.461 29776 1502 99.923 0.221 0.2186 0.2223 0.2718 0.2682 40.64
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] 3.581 -0.975 -2.605
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_dihedral_angle_4_deg 14.424 r_dihedral_angle_3_deg 14.312 r_lrange_it 8.429 r_lrange_other 8.402 r_scangle_it 6.804 r_scangle_other 6.803 r_dihedral_angle_1_deg 6.189 r_mcangle_it 5.421 r_mcangle_other 5.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.22 r_dihedral_angle_4_deg 14.424 r_dihedral_angle_3_deg 14.312 r_lrange_it 8.429 r_lrange_other 8.402 r_scangle_it 6.804 r_scangle_other 6.803 r_dihedral_angle_1_deg 6.189 r_mcangle_it 5.421 r_mcangle_other 5.42 r_scbond_it 4.59 r_scbond_other 4.589 r_mcbond_it 3.847 r_mcbond_other 3.845 r_angle_refined_deg 1.529 r_angle_other_deg 1.369 r_symmetry_xyhbond_nbd_refined 0.242 r_nbd_refined 0.212 r_nbd_other 0.192 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.181 r_nbtor_refined 0.168 r_symmetry_xyhbond_nbd_other 0.159 r_ncsr_local_group_2 0.102 r_ncsr_local_group_3 0.098 r_symmetry_nbd_refined 0.087 r_ncsr_local_group_4 0.087 r_chiral_restr 0.086 r_ncsr_local_group_1 0.079 r_ncsr_local_group_6 0.078 r_ncsr_local_group_5 0.077 r_symmetry_nbtor_other 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3875 Nucleic Acid Atoms Solvent Atoms 392 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing