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The de novo evolutionary emergence of a symmetrical protein is shaped by folding constraints
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.05 M PCB buffer (2:1:2 ratio of sodium propionate, sodium cacodylate and Bis-Tris propane, pH 7)
12% polyethylene glycol 1,500.
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.219 α = 90 b = 112.219 β = 90 c = 107.29 γ = 120
Symmetry Space Group P 31 1 2
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++ 2014-05-19 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) 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 1.65 50 100 6.7 6.7 92166
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.65 30.18 87992 4637 99.97 0.1893 0.18613 0.1986 0.24753 0.2541 RANDOM 16.546
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] -0.55 -0.55 -0.55 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.836 r_sphericity_free 18.52 r_dihedral_angle_3_deg 12.474 r_sphericity_bonded 9.089 r_dihedral_angle_4_deg 8.009 r_dihedral_angle_1_deg 6.799 r_rigid_bond_restr 5.818 r_angle_refined_deg 1.945 r_angle_other_deg 1.223 r_chiral_restr 0.197
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 21.836 r_sphericity_free 18.52 r_dihedral_angle_3_deg 12.474 r_sphericity_bonded 9.089 r_dihedral_angle_4_deg 8.009 r_dihedral_angle_1_deg 6.799 r_rigid_bond_restr 5.818 r_angle_refined_deg 1.945 r_angle_other_deg 1.223 r_chiral_restr 0.197 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 5636 Nucleic Acid Atoms Solvent Atoms 500 Heterogen Atoms 75
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing