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Structure of the tripod (BppUct-A-L) from the baseplate of bacteriophage Tuc2009
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5E7F 5E7F RBP domain
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.2 293 by mixing 300 nl of protein (Na2HPO4, 10 mM; KH2PO4, 1.8 mM [pH7.4]; NaCl, 137 mM; KCl, 2.7 mM) with 100 nl precipitant solution (2 M Ammonium Sulfate, 0.1 M Na Hepes [pH 7]).
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 211.96 α = 90 b = 211.96 β = 90 c = 211.96 γ = 90
Symmetry Space Group P 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 PIXEL PSI PILATUS 6M 2015-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.97 SOLEIL PROXIMA 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 2.9 34.9 99.8 0.187 10.7 13.7 70164 103.95
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 2.9 3 99.3 1.9 1.25 13.7
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 MOLECULAR REPLACEMENT THROUGHOUT 5E7F RBP domain 2.9 34.85 70164 3508 99.9 0.2155 0.2143 0.2247 0.2372 0.2454 RANDOM 104.51
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 t_other_torsion 20.66 t_omega_torsion 2.85 t_angle_deg 1.18 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 20.66 t_omega_torsion 2.85 t_angle_deg 1.18 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 8126 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 26
Software Software Software Name Purpose BUSTER refinement XDS data reduction XSCALE data scaling MOLREP phasing Coot model building