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Crystal structure of the engineered SsoPox variant IVB10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VC5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25% (w/v) PEG 8000 and Tris-HCl buffer (pH 8.5)
Crystal Properties Matthews coefficient Solvent content 2.38 48.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.26 α = 90 b = 74.69 β = 90 c = 138.71 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 EIGER X 16M 2017-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 1.03321 APS 23-ID-B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.5 49.19 100 0.055 0.999 21.5 8.25 54520
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 0.599 0.945 8.41
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 1.5 49.19 51793 2726 99.98 0.14022 0.13848 0.1429 0.17272 0.1763 RANDOM 22.579
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] 2.48 -1.31 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.569 r_rigid_bond_restr 5.448 r_long_range_B_refined 4.149 r_long_range_B_other 4.088 r_scangle_other 3.83 r_scbond_it 3.435 r_scbond_other 3.434 r_mcangle_it 2.565 r_mcangle_other 2.564
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.252 r_dihedral_angle_1_deg 6.569 r_rigid_bond_restr 5.448 r_long_range_B_refined 4.149 r_long_range_B_other 4.088 r_scangle_other 3.83 r_scbond_it 3.435 r_scbond_other 3.434 r_mcangle_it 2.565 r_mcangle_other 2.564 r_mcbond_it 2.247 r_dihedral_angle_2_deg 2.241 r_mcbond_other 2.231 r_angle_refined_deg 0.846 r_angle_other_deg 0.355 r_chiral_restr 0.044 r_bond_other_d 0.008 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2501 Nucleic Acid Atoms Solvent Atoms 316 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing