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NATIVE TAILSPIKE PROTEIN OF BACTERIOPHAGE SF6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBE PDB ENTRY 2VBE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 CRYSTALLIZATION CONDITIONS: VAPOR DIFFUSION HANGING DROP,20 DEGR. CELSIUS; DROP: 1 MICROL RESERVOIR AND 1 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.0,18% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.9 57.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.231 α = 90 b = 96.231 β = 90 c = 182.433 γ = 120
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 2000-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B EMBL/DESY, HAMBURG BW7B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.25 20 97.4 0.05 11.6 2.2 169746 9.19
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 79.8 0.25 2 1.9
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 2VBE 1.25 14.92 161221 8511 97.4 0.12 0.119 0.1333 0.142 0.1529 RANDOM 10.2
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 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.687 r_scangle_it 5.346 r_scbond_it 4.256 r_mcangle_it 3.415 r_mcbond_it 2.879 r_angle_other_deg 2.389 r_angle_refined_deg 1.664 r_symmetry_vdw_other 0.322 r_nbd_other 0.277 r_symmetry_vdw_refined 0.243
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.687 r_scangle_it 5.346 r_scbond_it 4.256 r_mcangle_it 3.415 r_mcbond_it 2.879 r_angle_other_deg 2.389 r_angle_refined_deg 1.664 r_symmetry_vdw_other 0.322 r_nbd_other 0.277 r_symmetry_vdw_refined 0.243 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.103 r_nbtor_other 0.091 r_gen_planes_other 0.009 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined 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 3833 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing