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Indirect contributions of mutations underlie optimization of new enzyme function
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EH9 PDB entry 5EH9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 291 25% (w/v) PEG 4 K, 20% (v/v) glycerol, 80 mM Tris-HCl, pH 8.5, 160 mM MgCl2
Crystal Properties Matthews coefficient Solvent content 2.14 42.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.638 α = 90 b = 55.735 β = 90 c = 79.878 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.0332 Australian Synchrotron MX2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.29 32.49 99.47 20.78 13.4 61760
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 5EH9 1.29 32.49 58628 3132 99.47 0.12796 0.12581 0.16805 0.1689 RANDOM 22.115
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] -0.74 1.24 -0.5
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 72.304 r_dihedral_angle_2_deg 30.809 r_dihedral_angle_4_deg 23.563 r_sphericity_bonded 20.871 r_dihedral_angle_3_deg 12.204 r_long_range_B_refined 8.875 r_long_range_B_other 8.875 r_dihedral_angle_1_deg 7.308 r_rigid_bond_restr 6.451 r_scangle_other 6.062
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 72.304 r_dihedral_angle_2_deg 30.809 r_dihedral_angle_4_deg 23.563 r_sphericity_bonded 20.871 r_dihedral_angle_3_deg 12.204 r_long_range_B_refined 8.875 r_long_range_B_other 8.875 r_dihedral_angle_1_deg 7.308 r_rigid_bond_restr 6.451 r_scangle_other 6.062 r_scbond_other 5.492 r_scbond_it 5.485 r_mcangle_it 3.791 r_mcangle_other 3.791 r_mcbond_it 3.22 r_mcbond_other 3.215 r_angle_refined_deg 2.203 r_angle_other_deg 1.292 r_chiral_restr 0.143 r_bond_refined_d 0.026 r_gen_planes_refined 0.014 r_gen_planes_other 0.014 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2002 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing