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Crystal structure of the stem and receptor binding domain of the spike protein P1 from bacteriophage PM2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VVD PDB ENTRY 2VVD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8 7.3MG/ML (IN 150MM NACL, 20MM TRIS PH 7.5, 10MM CACL2),20%(W/V) PEG6K,100MM TRIS PH 8, 200MM LICL
Crystal Properties Matthews coefficient Solvent content 2.24 45.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.894 α = 90 b = 107.894 β = 90 c = 44.171 γ = 90
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 MARRESEARCH MIRRORS 2006-08-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 ESRF BM14
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 1.77 23 94.9 0.08 30.2 11.2 47548 -3 21.1
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 1.77 1.83 71.8 0.87 1.8 7.1
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 2VVD 1.77 23 45122 2423 94.8 0.176 0.173 0.1717 0.226 0.2245 RANDOM 18.65
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] -0.12 -0.12 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_4_deg 16.637 r_dihedral_angle_3_deg 11.522 r_scangle_it 9.438 r_scbond_it 7.045 r_dihedral_angle_1_deg 6.863 r_mcangle_it 4.732 r_mcbond_it 3.807 r_angle_refined_deg 1.097 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.258 r_dihedral_angle_4_deg 16.637 r_dihedral_angle_3_deg 11.522 r_scangle_it 9.438 r_scbond_it 7.045 r_dihedral_angle_1_deg 6.863 r_mcangle_it 4.732 r_mcbond_it 3.807 r_angle_refined_deg 1.097 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.186 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.136 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.075 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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_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 3966 Nucleic Acid Atoms Solvent Atoms 539 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing