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Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen octasaccharide fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VBK PDB ENTRY 2VBK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 PROTEIN WAS CRYSTALLISED FROM 0.1 M MES, PH 6.5, 16 % PEG 8000, 20 MM MNCL2
Crystal Properties Matthews coefficient Solvent content 2.41 48.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.987 α = 90 b = 138.895 β = 92.05 c = 136.073 γ = 90
Symmetry Space Group P 1 21 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 CCD MARRESEARCH MIRRORS 2012-09-27 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) 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 1.95 46.3 99.7 0.24 6.2 4.5 224609 14.29
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 1.95 2.05 98.5 0.84 2.1 4.6
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 2VBK 1.95 45.33 223380 11044 99.87 0.1977 0.1957 0.1956 0.2358 0.2289 RANDOM 18.92
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] 0.5848 -0.7726 -2.1176 1.5328
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.18 t_omega_torsion 3.93 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.18 t_omega_torsion 3.93 t_angle_deg 1.16 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 22868 Nucleic Acid Atoms Solvent Atoms 1539 Heterogen Atoms 584
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing