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G14 variant of 57aBi scaffold crystallized in P6422
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 9THX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 28% (v/v) PEG 400,
0.2 M CaCl2,
0.1 M HEPES
Crystal Properties Matthews coefficient Solvent content 2.4 48.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.976 α = 90 b = 71.976 β = 90 c = 108.713 γ = 120
Symmetry Space Group P 64 2 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 PIXEL Bruker PHOTON II 2016-08-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.3418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.07 41.001 78.2 0.204 0.033 0.999 26.4 37.9 8369
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.21 22.9 3.503 0.681 0.522 26.1
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 (All) 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 2.07 41.001 8356 422 78.05 0.225 0.225 0.2215 0.2285 0.2869 0.29 RANDOM 45.973
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] 0.09 0.045 0.09 -0.291
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.501 r_dihedral_angle_6_deg 13.49 r_lrange_other 10.586 r_lrange_it 10.581 r_dihedral_angle_2_deg 10.008 r_scangle_it 8.089 r_scangle_other 8.084 r_dihedral_angle_1_deg 7.477 r_mcangle_it 6.531 r_mcangle_other 6.527
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.501 r_dihedral_angle_6_deg 13.49 r_lrange_other 10.586 r_lrange_it 10.581 r_dihedral_angle_2_deg 10.008 r_scangle_it 8.089 r_scangle_other 8.084 r_dihedral_angle_1_deg 7.477 r_mcangle_it 6.531 r_mcangle_other 6.527 r_scbond_it 5.284 r_scbond_other 5.279 r_mcbond_it 4.298 r_mcbond_other 4.295 r_angle_refined_deg 1.848 r_angle_other_deg 0.598 r_nbd_refined 0.219 r_nbtor_refined 0.197 r_symmetry_nbd_other 0.195 r_symmetry_xyhbond_nbd_refined 0.193 r_nbd_other 0.174 r_xyhbond_nbd_refined 0.171 r_symmetry_nbd_refined 0.158 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction STARANISO data scaling PHASER phasing