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SV40 VP1 pentamer in complex with GM1 oligosaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SVA PDB ENTRY 1SVA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 RESERVOIR: 0.1 M TRIS, PH 8.5, 24% PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30% ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.74 55.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.764 α = 90 b = 93.087 β = 105.6 c = 118.882 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2006-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.25 30 89.8 0.097 11.2 8.7 68387 33.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.33 53.8 0.276 1.9 4.8 4050
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 (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 PDB ENTRY 1SVA 2.25 29.76 68387 6868 89.8 0.19206 0.18743 0.1844 0.23318 0.2279 RANDOM 33.589
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] -2.26 -2.6 2.29 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_3_deg 13.741 r_dihedral_angle_4_deg 13.641 r_dihedral_angle_1_deg 5.514 r_scangle_it 4.006 r_mcangle_it 3.314 r_scbond_it 2.728 r_mcbond_it 2.082 r_angle_refined_deg 0.814 r_symmetry_vdw_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.474 r_dihedral_angle_3_deg 13.741 r_dihedral_angle_4_deg 13.641 r_dihedral_angle_1_deg 5.514 r_scangle_it 4.006 r_mcangle_it 3.314 r_scbond_it 2.728 r_mcbond_it 2.082 r_angle_refined_deg 0.814 r_symmetry_vdw_refined 0.32 r_nbtor_refined 0.309 r_nbd_refined 0.192 r_symmetry_hbond_refined 0.11 r_xyhbond_nbd_refined 0.104 r_bond_refined_d 0.005 r_chiral_restr 0.003 r_gen_planes_refined 0.002 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10160 Nucleic Acid Atoms Solvent Atoms 855 Heterogen Atoms 228
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing