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Crystal structure of VACV N1 protein
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 0.2 M Potassium sodium tartrate tetrahydrate, 0.1 M Tris pH 8.0, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 3.02 59.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.86 α = 90 b = 77.86 β = 90 c = 111.39 γ = 120
Symmetry Space Group P 61 2 2
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 2.42 42.94 99.9 0.999 24.5 35.7 8116
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 2.42 2.51 0.911
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.42 42.94 8092 405 99.84 0.172 0.1701 0.179 0.2062 0.2058 43.187
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] 0.969 0.484 0.969 -3.143
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.98 r_dihedral_angle_3_deg 12.65 r_dihedral_angle_4_deg 12.452 r_lrange_other 8.442 r_lrange_it 8.436 r_scangle_it 6.615 r_scangle_other 6.613 r_dihedral_angle_1_deg 6.466 r_mcangle_other 5.164 r_mcangle_it 5.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.98 r_dihedral_angle_3_deg 12.65 r_dihedral_angle_4_deg 12.452 r_lrange_other 8.442 r_lrange_it 8.436 r_scangle_it 6.615 r_scangle_other 6.613 r_dihedral_angle_1_deg 6.466 r_mcangle_other 5.164 r_mcangle_it 5.162 r_scbond_it 4.81 r_scbond_other 4.778 r_mcbond_it 3.776 r_mcbond_other 3.763 r_angle_refined_deg 1.66 r_angle_other_deg 1.412 r_nbd_refined 0.211 r_nbd_other 0.202 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.168 r_symmetry_xyhbond_nbd_refined 0.152 r_symmetry_nbd_refined 0.108 r_chiral_restr 0.089 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.01 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 1014 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing