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TAILSPIKE PROTEIN OF E.COLI BACTERIOPHAGE HK620 IN COMPLEX WITH HEXASACCHARIDE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VJI PDB ENTRY 2VJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 VAPOR DIFFUSION, HANGING DROP: PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH8.0, 2 MM EDTA,0.2M NACL.RERVOIR: 20% ISOPROPANOL,0.1 M NA-ACETATE,PH6.0,0.2M CACL2. DROPLET 1.5:1.5 MICRO LITER. 30MM HEXASACCHARIDE. CRYO:30% GLYCEROL.TEMPERATURE 20 DEGREE CELSIUS.
Crystal Properties Matthews coefficient Solvent content 2.15 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.91 α = 90 b = 73.91 β = 90 c = 174.59 γ = 120
Symmetry Space Group P 3 2 1
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 2006-04-19 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 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 1.58 19.2 95.6 0.04 26.7 83.5 73235 10.9
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 1.58 1.64 83.5 0.13 10.9 4.1
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 2VJI 1.59 43.64 69829 3711 96.9 0.134 0.133 0.1414 0.165 0.17 RANDOM 8.74
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] 0.23 0.12 0.23 -0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_3_deg 11.337 r_scangle_it 7.812 r_dihedral_angle_1_deg 7.069 r_scbond_it 5.217 r_mcangle_it 3.162 r_mcbond_it 2.292 r_angle_other_deg 1.772 r_angle_refined_deg 1.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_3_deg 11.337 r_scangle_it 7.812 r_dihedral_angle_1_deg 7.069 r_scbond_it 5.217 r_mcangle_it 3.162 r_mcbond_it 2.292 r_angle_other_deg 1.772 r_angle_refined_deg 1.303 r_symmetry_vdw_other 0.264 r_nbd_refined 0.252 r_nbd_other 0.221 r_symmetry_vdw_refined 0.196 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.139 r_symmetry_hbond_refined 0.136 r_nbtor_other 0.102 r_chiral_restr 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 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 4536 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing