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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 3DHB PDB entry 3DHB
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 2.1 41.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.511 α = 90 b = 55.473 β = 90 c = 79.358 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 45.47 99.8 16.33 7 61128
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 3DHB 1.29 45.47 58033 3094 99.8 0.11693 0.11503 0.15347 0.1548 RANDOM 24.686
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] -0.32 1.5 -1.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.8 r_dihedral_angle_2_deg 29.144 r_dihedral_angle_4_deg 23.889 r_sphericity_bonded 20.743 r_dihedral_angle_3_deg 11.111 r_long_range_B_refined 7.616 r_long_range_B_other 7.615 r_dihedral_angle_1_deg 6.837 r_rigid_bond_restr 6.809 r_scangle_other 6.688
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 54.8 r_dihedral_angle_2_deg 29.144 r_dihedral_angle_4_deg 23.889 r_sphericity_bonded 20.743 r_dihedral_angle_3_deg 11.111 r_long_range_B_refined 7.616 r_long_range_B_other 7.615 r_dihedral_angle_1_deg 6.837 r_rigid_bond_restr 6.809 r_scangle_other 6.688 r_scbond_it 6.027 r_scbond_other 6.027 r_mcangle_it 4.652 r_mcangle_other 4.651 r_mcbond_it 3.883 r_mcbond_other 3.883 r_angle_refined_deg 2.244 r_angle_other_deg 1.367 r_chiral_restr 0.163 r_bond_refined_d 0.026 r_gen_planes_other 0.015 r_gen_planes_refined 0.013 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 2007 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing