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Computationally designed C3-symmetric homotrimer from TPR repeat protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model designed model from rosetta
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 1M LiCl
100mM citrate
20% w/v PEG 6000
pH 4
Crystal Properties Matthews coefficient Solvent content 2.59 52.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.47 α = 90 b = 64.91 β = 106.33 c = 99.03 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC QUANTUM 315r 2016-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.53 38.9 99.83 0.1427 0.1608 0.07334 0.994 9.5 4.6 28508 37.11
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 2.53 2.62 99.89 0.8023 0.9033 0.4106 0.729 2.16 4.6
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 designed model from rosetta 2.53 38.87 27066 1442 99.86 0.18821 0.18591 0.1946 0.23166 0.2403 RANDOM 51.943
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] -0.59 0.79 -0.2 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 21.408 r_dihedral_angle_3_deg 18.139 r_long_range_B_other 10.896 r_long_range_B_refined 10.894 r_scangle_other 9.618 r_scbond_it 6.955 r_scbond_other 6.954 r_mcangle_it 5.998 r_mcangle_other 5.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.724 r_dihedral_angle_4_deg 21.408 r_dihedral_angle_3_deg 18.139 r_long_range_B_other 10.896 r_long_range_B_refined 10.894 r_scangle_other 9.618 r_scbond_it 6.955 r_scbond_other 6.954 r_mcangle_it 5.998 r_mcangle_other 5.997 r_dihedral_angle_1_deg 5.105 r_mcbond_it 4.407 r_mcbond_other 4.407 r_angle_refined_deg 1.468 r_angle_other_deg 1.225 r_chiral_restr 0.098 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5848 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data reduction HKL-2000 data scaling PHASER phasing