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Crystal structure of Wild Type Cypovirus Polyhedra produced by cell-free protein synthesis with small volume
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 24.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 103.6 α = 90 b = 103.6 β = 90 c = 103.6 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 2022-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL32XU 1 SPring-8 BL32XU
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 1.95 50 100 0.9908 7.3 447.7 13641
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 1.95 1.96 100 0.6707 1.23
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 1.95 42.295 13624 1372 99.985 0.171 0.1659 0.177 0.2157 0.2149 20.483
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 34.904 r_dihedral_angle_4_deg 22.601 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 7.657 r_lrange_it 3.223 r_lrange_other 3.172 r_scangle_it 2.426 r_scangle_other 2.422 r_mcangle_it 1.64 r_mcangle_other 1.639
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.904 r_dihedral_angle_4_deg 22.601 r_dihedral_angle_3_deg 12.989 r_dihedral_angle_1_deg 7.657 r_lrange_it 3.223 r_lrange_other 3.172 r_scangle_it 2.426 r_scangle_other 2.422 r_mcangle_it 1.64 r_mcangle_other 1.639 r_scbond_it 1.603 r_scbond_other 1.602 r_angle_refined_deg 1.442 r_angle_other_deg 1.34 r_mcbond_it 1.177 r_mcbond_other 1.172 r_nbd_other 0.235 r_symmetry_nbd_refined 0.223 r_nbd_refined 0.192 r_symmetry_nbd_other 0.173 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.155 r_xyhbond_nbd_refined 0.121 r_symmetry_nbtor_other 0.073 r_chiral_restr 0.071 r_bond_refined_d 0.007 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 2006 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PHENIX refinement CrystFEL data scaling Coot model building XDS data reduction PHASER phasing