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The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TL2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 292 0.1M NaF,
0.05 M Bis-Tris propane pH 7.5,
10% polyethylene glycol 3,350.
Crystal Properties Matthews coefficient Solvent content 2.14 42.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.693 α = 90 b = 60.929 β = 90 c = 88.351 γ = 90
Symmetry Space Group P 21 21 21
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 RIGAKU RAXIS IV++ 2009-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5417
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 1.9 50 99.8 0.042 29.6 6.1 19656 24.1
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 1.9 1.93 97.4 0.303 2.6 4.2
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 1TL2 1.9 50 18599 1002 99.77 0.1929 0.19068 0.1965 0.23485 0.2465 RANDOM 20.718
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] 1 -0.5 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 14.51 r_dihedral_angle_1_deg 11.044 r_sphericity_free 9.711 r_scangle_it 5.132 r_sphericity_bonded 4.64 r_scbond_it 3.727 r_mcangle_it 2.567 r_rigid_bond_restr 2.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30 r_dihedral_angle_4_deg 19.608 r_dihedral_angle_3_deg 14.51 r_dihedral_angle_1_deg 11.044 r_sphericity_free 9.711 r_scangle_it 5.132 r_sphericity_bonded 4.64 r_scbond_it 3.727 r_mcangle_it 2.567 r_rigid_bond_restr 2.389 r_angle_refined_deg 1.902 r_mcbond_it 1.637 r_chiral_restr 0.158 r_bond_refined_d 0.024 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other35.9 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1876 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing