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Siphovirus 9NA tailspike receptor binding domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 293 20% PEG 5000 MME, 0.1M BisTris pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 149.132 α = 90 b = 149.132 β = 90 c = 149.132 γ = 90
Symmetry Space Group I 21 3
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 RAYONIX MX-225 2010-11-23 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) 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 1.5 33.3 99.7 0.071 0.065 15.6 4.6 87485 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.54 99.7 0.755 0.686 2.59 1.1
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2VFM 1.5 33.35 87485 83067 4372 100 0.12984 0.12773 0.1695 0.1616 RANDOM 19.858
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_1_deg 6.618 r_scangle_it 4.818 r_scbond_it 3.386 r_mcangle_it 2.154 r_rigid_bond_restr 1.611 r_angle_refined_deg 1.43 r_mcbond_it 1.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.184 r_dihedral_angle_4_deg 12.404 r_dihedral_angle_3_deg 11.505 r_dihedral_angle_1_deg 6.618 r_scangle_it 4.818 r_scbond_it 3.386 r_mcangle_it 2.154 r_rigid_bond_restr 1.611 r_angle_refined_deg 1.43 r_mcbond_it 1.402 r_chiral_restr 0.107 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4154 Nucleic Acid Atoms Solvent Atoms 701 Heterogen Atoms 6
Software Software Software Name Purpose XDS data scaling PHASER phasing REFMAC refinement XDS data reduction