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Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GQM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 293 cell-free crystallization
Crystal Properties Matthews coefficient Solvent content 1.63 24.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.61 α = 90 b = 103.61 β = 90 c = 103.61 γ = 90
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 PILATUS3 6M 2021-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 1.8 50 100 0.9899 5.5 399 17297
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 1.8 1.81 0.5326 1.53
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 5gqm 1.801 42.299 17297 1742 99.988 0.153 0.1495 0.1611 0.184 0.1953 15.194
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 r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 12.359 r_dihedral_angle_1_deg 7.366 r_lrange_it 3.389 r_lrange_other 3.318 r_scangle_it 2.511 r_scangle_other 2.511 r_scbond_other 1.635 r_scbond_it 1.633
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.342 r_dihedral_angle_4_deg 21.503 r_dihedral_angle_3_deg 12.359 r_dihedral_angle_1_deg 7.366 r_lrange_it 3.389 r_lrange_other 3.318 r_scangle_it 2.511 r_scangle_other 2.511 r_scbond_other 1.635 r_scbond_it 1.633 r_angle_refined_deg 1.53 r_angle_other_deg 1.398 r_mcangle_it 1.389 r_mcangle_other 1.389 r_mcbond_it 0.963 r_mcbond_other 0.961 r_symmetry_nbd_refined 0.219 r_nbd_other 0.2 r_nbd_refined 0.195 r_symmetry_nbd_other 0.172 r_nbtor_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.126 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.077 r_symmetry_nbtor_other 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2006 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrystFEL data scaling Coot model building XDS data reduction PHASER phasing