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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 7.5 293 0.2M MgCl2 6H2O
0.1M Tris pH=7.5
20% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.44 49.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 156.749 α = 90 b = 53.09 β = 106.81 c = 89.23 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++ 2017-09-04 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 1.9 41.47 99.91 0.09026 5.56 3.3 55705 18.19
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 1.9 1.968 99.87 0.4785 1.49 3.1
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 1HYZ 1.9 41.47 52891 2784 99.92 0.18369 0.1822 0.1909 0.21197 0.2182 RANDOM 18.901
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] -0.69 -0.41 2.33 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.751 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_1_deg 6.693 r_long_range_B_refined 3.713 r_long_range_B_other 3.665 r_scangle_other 3.037 r_scbond_other 1.986 r_scbond_it 1.985 r_mcangle_it 1.842
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.751 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 12.856 r_dihedral_angle_1_deg 6.693 r_long_range_B_refined 3.713 r_long_range_B_other 3.665 r_scangle_other 3.037 r_scbond_other 1.986 r_scbond_it 1.985 r_mcangle_it 1.842 r_mcangle_other 1.841 r_angle_refined_deg 1.608 r_mcbond_it 1.232 r_mcbond_other 1.232 r_angle_other_deg 0.516 r_chiral_restr 0.104 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 5035 Nucleic Acid Atoms Solvent Atoms 284 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing