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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 2.41 48.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.451 α = 90 b = 69.451 β = 90 c = 117.227 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 2.19 33.32 78.7 0.188 0.058 0.997 11.3 10.1 7219
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 2.19 2.36 23.6 2.162 0.637 0.694 11.5
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 2.19 33.318 7210 364 78.867 0.235 0.235 0.2324 0.2388 0.2828 0.2729 RANDOM 46.992
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] 0.218 0.109 0.218 -0.706
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.069 r_dihedral_angle_6_deg 15.486 r_lrange_it 8.798 r_lrange_other 8.775 r_dihedral_angle_2_deg 8.729 r_dihedral_angle_1_deg 7.2 r_scangle_it 6.954 r_scangle_other 6.949 r_mcangle_it 6.159 r_mcangle_other 6.155
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.069 r_dihedral_angle_6_deg 15.486 r_lrange_it 8.798 r_lrange_other 8.775 r_dihedral_angle_2_deg 8.729 r_dihedral_angle_1_deg 7.2 r_scangle_it 6.954 r_scangle_other 6.949 r_mcangle_it 6.159 r_mcangle_other 6.155 r_scbond_it 4.506 r_scbond_other 4.502 r_mcbond_it 4.368 r_mcbond_other 4.361 r_angle_refined_deg 1.688 r_angle_other_deg 0.532 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.219 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.176 r_nbd_other 0.152 r_symmetry_nbd_refined 0.125 r_symmetry_nbtor_other 0.09 r_chiral_restr 0.073 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1007 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement STARANISO data scaling XDS data reduction PHASER phasing