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Structure of Goose Hemorrhagic Polyomavirus VP1 in complex with 2-O-Methyl-5-N-acetyl-alpha-D-neuraminic acid
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 formate, ammonium acetate, Na citrate tribasic, Na oxamate, Na K tartrate, MES, imidazole, PEG 8000, ethylene glycol
Crystal Properties Matthews coefficient Solvent content 2.41 48.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.46 α = 94.232 b = 90.54 β = 98.09 c = 101.22 γ = 107.867
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 1.95 49.58 97.71 0.1468 0.993 9.38 3.6 206886 18.43
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 1.95 2.02 0.7611 0.701 2.02
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 1.95 49.577 206888 2069 97.724 0.166 0.1652 0.173 0.2008 0.2065 17.311
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] 0.879 -0.053 -1.35 0.141 -1.315
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.982 r_dihedral_angle_4_deg 18.975 r_dihedral_angle_3_deg 11.479 r_dihedral_angle_1_deg 7.652 r_lrange_it 4.643 r_lrange_other 4.643 r_scangle_it 2.67 r_scangle_other 2.67 r_mcangle_it 2.002 r_mcangle_other 2.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.982 r_dihedral_angle_4_deg 18.975 r_dihedral_angle_3_deg 11.479 r_dihedral_angle_1_deg 7.652 r_lrange_it 4.643 r_lrange_other 4.643 r_scangle_it 2.67 r_scangle_other 2.67 r_mcangle_it 2.002 r_mcangle_other 2.002 r_scbond_it 1.773 r_scbond_other 1.773 r_angle_refined_deg 1.467 r_angle_other_deg 1.333 r_mcbond_it 1.321 r_mcbond_other 1.32 r_nbd_other 0.308 r_symmetry_nbd_refined 0.276 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.187 r_nbd_refined 0.186 r_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.159 r_symmetry_xyhbond_nbd_other 0.155 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.068 r_ncsr_local_group_25 0.053 r_ncsr_local_group_21 0.051 r_ncsr_local_group_27 0.05 r_ncsr_local_group_34 0.049 r_ncsr_local_group_35 0.049 r_ncsr_local_group_6 0.048 r_ncsr_local_group_11 0.047 r_ncsr_local_group_15 0.047 r_ncsr_local_group_28 0.047 r_ncsr_local_group_33 0.047 r_ncsr_local_group_18 0.046 r_ncsr_local_group_4 0.045 r_ncsr_local_group_17 0.045 r_ncsr_local_group_2 0.044 r_ncsr_local_group_7 0.044 r_ncsr_local_group_23 0.044 r_ncsr_local_group_24 0.044 r_ncsr_local_group_30 0.044 r_ncsr_local_group_20 0.043 r_ncsr_local_group_22 0.043 r_ncsr_local_group_32 0.043 r_ncsr_local_group_37 0.043 r_ncsr_local_group_3 0.042 r_ncsr_local_group_10 0.042 r_ncsr_local_group_14 0.042 r_ncsr_local_group_19 0.042 r_ncsr_local_group_26 0.042 r_ncsr_local_group_31 0.042 r_ncsr_local_group_40 0.042 r_ncsr_local_group_36 0.041 r_ncsr_local_group_41 0.041 r_ncsr_local_group_42 0.041 r_ncsr_local_group_1 0.04 r_ncsr_local_group_9 0.04 r_ncsr_local_group_16 0.04 r_ncsr_local_group_44 0.039 r_ncsr_local_group_45 0.039 r_ncsr_local_group_29 0.038 r_ncsr_local_group_13 0.037 r_ncsr_local_group_39 0.036 r_ncsr_local_group_43 0.036 r_ncsr_local_group_8 0.034 r_ncsr_local_group_12 0.031 r_ncsr_local_group_38 0.031 r_ncsr_local_group_5 0.03 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 20026 Nucleic Acid Atoms Solvent Atoms 2665 Heterogen Atoms 333
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing Coot model building