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Full-length Tailspike Protein Mutant Y108W of Bacteriophage P22
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VNL PDB ENTRIES 2VNL AND 2VFM experimental model PDB 2VFM PDB ENTRIES 2VNL AND 2VFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 PROTEIN- 15MG/ML IN 10MM HEPES PH7;RESERVOIR:750 ML 0.2M AMMONIUM ACETATE,0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.6, 30% W/V POLYETHYLENE GLYCOL 4000; HANGING DROPS:1.5MICROL RESERVOIR- 1.5MICROL PROTEIN SOLUTION; TEMPERATURE: 19 DEGR.; CRYO: 3% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.51 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.358 α = 90 b = 121.558 β = 90 c = 208.255 γ = 90
Symmetry Space Group P 21 21 21
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 MIRRORS 2008-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 BESSY 14.1
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 1.65 48.3 90.4 0.1 12.5 6.3 237282 -3 20
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 1.65 1.85 68.3 0.45 2.3 2.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2VNL AND 2VFM 1.65 49.45 228771 12041 91.73 0.16756 0.16532 0.21038 0.1986 RANDOM 8.822
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] -0.01 0.05 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.059 r_dihedral_angle_4_deg 12.401 r_dihedral_angle_3_deg 12.303 r_dihedral_angle_1_deg 6.619 r_scangle_it 5.315 r_scbond_it 3.834 r_mcangle_it 2.508 r_mcbond_it 1.791 r_angle_refined_deg 1.366 r_angle_other_deg 0.836
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.059 r_dihedral_angle_4_deg 12.401 r_dihedral_angle_3_deg 12.303 r_dihedral_angle_1_deg 6.619 r_scangle_it 5.315 r_scbond_it 3.834 r_mcangle_it 2.508 r_mcbond_it 1.791 r_angle_refined_deg 1.366 r_angle_other_deg 0.836 r_mcbond_other 0.658 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 15064 Nucleic Acid Atoms Solvent Atoms 2265 Heterogen Atoms 131
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling AMoRE phasing