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Structure of free SV40 VP1 pentamer
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 273 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 273K
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 154.04 α = 90 b = 93.66 β = 105.54 c = 120.81 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 2.3 50 86.8 0.099 6.7 4.8 73715 63985
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 2.3 2.38 52.2 0.26 1.4 3.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 2.3 39.78 73715 57548 6346 86.81 0.21217 0.20746 0.2069 0.2542 0.2506 RANDOM 39.406
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] -3.43 -3.75 4.92 -3.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.269 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.04 r_mcangle_it 3.718 r_scbond_it 2.906 r_mcbond_it 2.391 r_angle_refined_deg 0.748 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.269 r_dihedral_angle_4_deg 18.159 r_dihedral_angle_3_deg 14.83 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.04 r_mcangle_it 3.718 r_scbond_it 2.906 r_mcbond_it 2.391 r_angle_refined_deg 0.748 r_nbtor_refined 0.312 r_nbd_refined 0.216 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.136 r_symmetry_hbond_refined 0.117 r_bond_refined_d 0.005 r_chiral_restr 0.002 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 10164 Nucleic Acid Atoms Solvent Atoms 676 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing