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Crystal structure of Symfoil-4T Permutation #1: de novo designed beta-trefoil architecture with symmetric primary structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3O4B PDB entry 3O4B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1.9 M ammonium sulfate, 0.2 M lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.04 39.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.667 α = 90 b = 56.667 β = 90 c = 81.102 γ = 90
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 MAR CCD 165 mm Osmic confocal 2010-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH2R 1.5418
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 2.2 40 92 13099 12051 1 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 2.2 2.26 57.9 0.331 4.64 2.2 636
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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 PDB entry 3O4B 2.2 23.226 2 13099 11928 585 91.28 0.2017 0.1988 0.1951 0.2569 0.2504 RANDOM 40.2462
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] -4.9857 -4.9857 9.9714
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.833 f_angle_d 0.571 f_chiral_restr 0.041 f_bond_d 0.003 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1933 Nucleic Acid Atoms Solvent Atoms 72 Heterogen Atoms 56
Software Software Software Name Purpose SCALEPACK data scaling PHENIX refinement PDB_EXTRACT data extraction HKL-2000 data collection DENZO data reduction PHENIX phasing