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Catalytic Improvement of an Artificial Metalloenzyme by Computational Design
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ZP9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.9 298 2.6 M ammonium sulfate, 50 mM Tris-HCl
Crystal Properties Matthews coefficient Solvent content 2.11 41.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.308 α = 90 b = 41.689 β = 104.26 c = 72.343 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M 2015-02-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.30510 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.6 70.11 90.3 0.096 0.048 0.996 11.6 4.7 29218
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 55.4 0.719 0.401 0.482 2.1 3.8 877
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 3ZP9 1.6 70.11 27665 1542 89.79 0.14008 0.13717 0.1366 0.19358 0.1941 RANDOM 18.147
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] 0.02 0.57 -0.57 0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.022 r_dihedral_angle_4_deg 24.221 r_sphericity_free 18.156 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 7.109 r_sphericity_bonded 6.809 r_long_range_B_refined 3.748 r_long_range_B_other 3.089 r_rigid_bond_restr 3.012 r_scbond_it 2.988
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.022 r_dihedral_angle_4_deg 24.221 r_sphericity_free 18.156 r_dihedral_angle_3_deg 13.03 r_dihedral_angle_1_deg 7.109 r_sphericity_bonded 6.809 r_long_range_B_refined 3.748 r_long_range_B_other 3.089 r_rigid_bond_restr 3.012 r_scbond_it 2.988 r_scangle_other 2.796 r_scbond_other 2.562 r_mcangle_it 2.233 r_mcangle_other 2.232 r_mcbond_it 2.092 r_mcbond_other 2.035 r_angle_refined_deg 1.838 r_angle_other_deg 1.004 r_chiral_restr 0.115 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 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 2059 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction