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Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HYZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.4 293 0.2M Magnesium acetate 4H2O
0.1M Na cacodylate pH=6.4
16% PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 155.797 α = 90 b = 53.56 β = 107.21 c = 89.339 γ = 90
Symmetry Space Group C 1 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2017-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5419
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.95 41.61 87.83 0.04564 10.91 7.4 45387 18.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.95 2.02 77.54 0.2236 3.05 7.3
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 1HYZ 1.95 41.61 43111 2272 87.83 0.17959 0.17743 0.1862 0.21957 0.2273 RANDOM 18.693
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] -1.09 -0.46 2.66 -1.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.518 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 3.805 r_long_range_B_other 3.8 r_scangle_other 2.906 r_mcangle_it 1.862 r_mcangle_other 1.862 r_scbond_it 1.826
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.518 r_dihedral_angle_4_deg 18.193 r_dihedral_angle_3_deg 13.997 r_dihedral_angle_1_deg 6.63 r_long_range_B_refined 3.805 r_long_range_B_other 3.8 r_scangle_other 2.906 r_mcangle_it 1.862 r_mcangle_other 1.862 r_scbond_it 1.826 r_scbond_other 1.826 r_angle_refined_deg 1.482 r_mcbond_it 1.237 r_mcbond_other 1.236 r_angle_other_deg 0.507 r_chiral_restr 0.064 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5033 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing