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Tailspike protein of bacteriophage Sf6 complexed with tetrasaccharide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBK PDB ENTRY 2VBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 VAPOR DIFFUSION HANGING DROP, 20 DEGR. CELSIUS; DROP: 3 MICROL RESERVOIR AND 3 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.5, 16% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, OCTASACCHARIDE CONCENTRATION/PROTEIN CONCENTATION 10:1; CRYOCONDITION: 0.1M MES, PH6.5, 25% PEG8000, 20MM MNCL2, 15% ETHYLENGLYCOL
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.358 α = 90 b = 95.358 β = 90 c = 182.765 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MARRESEARCH MIRRORS 2005-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 47.7 99.7 0.06 17.4 4.9 39641 17.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.07 97.2 0.22 7 4
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 2VBK 2 47.67 39641 2110 99.8 0.192 0.19 0.1988 0.232 0.2358 RANDOM 20.2
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] 0.36 0.18 0.36 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 12.96 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 6.767 r_scangle_it 2.843 r_scbond_it 2.086 r_angle_refined_deg 1.362 r_mcangle_it 1.108 r_mcbond_it 0.826 r_angle_other_deg 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.978 r_dihedral_angle_4_deg 12.96 r_dihedral_angle_3_deg 12.676 r_dihedral_angle_1_deg 6.767 r_scangle_it 2.843 r_scbond_it 2.086 r_angle_refined_deg 1.362 r_mcangle_it 1.108 r_mcbond_it 0.826 r_angle_other_deg 0.766 r_symmetry_vdw_other 0.221 r_nbd_other 0.187 r_nbd_refined 0.181 r_nbtor_refined 0.168 r_symmetry_hbond_refined 0.149 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.136 r_nbtor_other 0.095 r_chiral_restr 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3821 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling AMoRE phasing