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Computationally designed left-handed alpha/alpha toroid with 3 repeats in space group P212121
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Rosetta Design
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 30% PEG 3350, 0.2M Sodium Chloride, 100mM Tris pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.139 α = 90 b = 68.603 β = 90 c = 152.357 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 CCD RIGAKU SATURN 944+ 2014-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.85 50 90.8 0.056 0.063 0.028 18.4 6 30892
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 95.9 0.5 0.541 0.203 0.951 7 3181
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 Rosetta Design 1.854 50 29249 1562 90.6 0.2305 0.2278 0.2366 0.2833 0.289 RANDOM 42.074
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] 1.82 1.02 -2.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_1_deg 4.776 r_mcangle_it 4.361 r_mcbond_it 3.333 r_mcbond_other 3.333 r_angle_refined_deg 1.721 r_angle_other_deg 1.624 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.598 r_dihedral_angle_3_deg 15.902 r_dihedral_angle_4_deg 15.146 r_dihedral_angle_1_deg 4.776 r_mcangle_it 4.361 r_mcbond_it 3.333 r_mcbond_other 3.333 r_angle_refined_deg 1.721 r_angle_other_deg 1.624 r_chiral_restr 0.095 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3038 Nucleic Acid Atoms Solvent Atoms 139 Heterogen Atoms 8
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction Coot model building PHASER phasing