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Structure of apo Goose Hemorrhagic Polyomavirus VP1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4FMG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 Na nitrate, Na phosphate dibasic, ammonium sulfate, MES, imidazole, PEG 8000, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.39 48.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.29 α = 94.048 b = 90.41 β = 97.898 c = 100.84 γ = 108.064
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 PIXEL DECTRIS PILATUS 2M-F 2017-01-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00 SLS X06DA
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 1.45 45.97 95.36 0.068 0.999 14.26 3.6 487522 12.8
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 1.45 1.502 0.702 0.797 2.16
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 4FMG 1.45 45.97 487470 4875 95.379 0.149 0.1484 0.1581 0.1703 0.1792 13.236
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] 0.648 -0.208 -0.707 0.117 -0.675 -0.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.995 r_dihedral_angle_4_deg 19.136 r_dihedral_angle_3_deg 10.905 r_dihedral_angle_1_deg 7.581 r_lrange_it 4.578 r_lrange_other 4.578 r_scangle_it 1.847 r_scangle_other 1.847 r_angle_refined_deg 1.513 r_angle_other_deg 1.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.995 r_dihedral_angle_4_deg 19.136 r_dihedral_angle_3_deg 10.905 r_dihedral_angle_1_deg 7.581 r_lrange_it 4.578 r_lrange_other 4.578 r_scangle_it 1.847 r_scangle_other 1.847 r_angle_refined_deg 1.513 r_angle_other_deg 1.421 r_mcangle_it 1.402 r_mcangle_other 1.402 r_scbond_it 1.217 r_scbond_other 1.217 r_mcbond_it 0.862 r_mcbond_other 0.861 r_symmetry_nbd_refined 0.306 r_nbd_other 0.208 r_nbd_refined 0.195 r_symmetry_nbd_other 0.184 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_other 0.148 r_symmetry_xyhbond_nbd_refined 0.119 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20009 Nucleic Acid Atoms Solvent Atoms 3289 Heterogen Atoms 434
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building