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Streptavidin WT artificial metalloenzyme for carboamination
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PK2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 298 2.0 M ammonium sulfate
0.1 M sodium acetate
-> soaking experiment by pH adjustment to pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.82 α = 90 b = 57.82 β = 90 c = 184.462 γ = 90
Symmetry Space Group I 41 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 DECTRIS EIGER X 16M 2020-08-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0000305674358714 SLS X06SA
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 1.48 46.158 99.9 0.117 0.123 0.038 0.998 14.2 19.3 26459
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 1.48 1.51 1.589 1.716 0.637 0.612 13.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.484 46.158 26428 1354 99.898 0.181 0.1795 0.1783 0.2021 0.2004 22.298
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] -0.052 -0.052 0.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.856 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_2_deg 8.909 r_lrange_it 8.604 r_lrange_other 7.94 r_dihedral_angle_1_deg 7.515 r_scangle_it 4.952 r_scangle_other 3.967 r_scbond_it 3.353 r_mcangle_it 3.324
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 13.856 r_dihedral_angle_3_deg 12.315 r_dihedral_angle_2_deg 8.909 r_lrange_it 8.604 r_lrange_other 7.94 r_dihedral_angle_1_deg 7.515 r_scangle_it 4.952 r_scangle_other 3.967 r_scbond_it 3.353 r_mcangle_it 3.324 r_mcangle_other 3.323 r_scbond_other 2.748 r_mcbond_it 2.281 r_mcbond_other 2.258 r_angle_refined_deg 2.004 r_angle_other_deg 0.684 r_xyhbond_nbd_refined 0.229 r_symmetry_nbd_other 0.202 r_nbd_refined 0.194 r_nbtor_refined 0.189 r_nbd_other 0.177 r_symmetry_xyhbond_nbd_refined 0.142 r_symmetry_xyhbond_nbd_other 0.113 r_chiral_restr 0.102 r_symmetry_nbd_refined 0.092 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 920 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 41
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing