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Crystal structure of SUWA (Super WA20), a hyper-stable de novo protein with a dimeric bisecting topology
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293.15 0.1M HEPES, 25% w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 1.92 35.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.636 α = 90 b = 71.93 β = 90 c = 81.563 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 95 CCD ADSC QUANTUM 315r Collimating Mirror-Monochromator-Focusing Mirror 2016-02-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
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 2 50 99.6 0.047 0.05 0.019 14.9 7.1 26639 38.9
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 2.07 100 0.629 0.679 0.252 0.867 2.77 7.1
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 3VJF 2 31.23 25230 1358 99.57 0.226 0.223 0.228 0.2837 0.294 RANDOM 48.908
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] 1.68 -1.25 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.463 r_dihedral_angle_4_deg 19.643 r_dihedral_angle_3_deg 17.87 r_dihedral_angle_1_deg 4.915 r_angle_other_deg 1.459 r_angle_refined_deg 1.341 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.463 r_dihedral_angle_4_deg 19.643 r_dihedral_angle_3_deg 17.87 r_dihedral_angle_1_deg 4.915 r_angle_other_deg 1.459 r_angle_refined_deg 1.341 r_chiral_restr 0.077 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3362 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MR-Rosetta phasing