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Crystal structure of the receptor binding domain of the spike protein P1 from bacteriophage PM2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 7.4MG/ML PROTEIN (IN 150MM NACL AND 20MM TRIS PH 7.5), 20%(W/V) PEG3350, 200MM CACL2
Crystal Properties Matthews coefficient Solvent content 1.94 36.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.645 α = 90 b = 49.055 β = 90 c = 72.177 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 MARRESEARCH MIRRORS 2005-06-22 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97912,0.90499 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 2.26 21.6 90 0.05 46.5 12.1 6935 -3 14.65
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 2.26 2.33 52.5 0.08 27.7 7.7
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 MAD THROUGHOUT NONE 2.26 21.6 6521 369 89.8 0.172 0.169 0.1787 0.228 0.1642 RANDOM 16.3
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] -0.59 0.23 0.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 11.205 r_dihedral_angle_1_deg 6.21 r_scangle_it 1.25 r_angle_refined_deg 0.966 r_scbond_it 0.887 r_angle_other_deg 0.77 r_mcangle_it 0.455 r_mcbond_it 0.259
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.875 r_dihedral_angle_4_deg 17.924 r_dihedral_angle_3_deg 11.205 r_dihedral_angle_1_deg 6.21 r_scangle_it 1.25 r_angle_refined_deg 0.966 r_scbond_it 0.887 r_angle_other_deg 0.77 r_mcangle_it 0.455 r_mcbond_it 0.259 r_symmetry_vdw_other 0.19 r_nbd_other 0.188 r_nbd_refined 0.181 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.12 r_symmetry_vdw_refined 0.119 r_xyhbond_nbd_refined 0.117 r_nbtor_other 0.078 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 1284 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing