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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 2.06 40.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.914 α = 90 b = 41.297 β = 104.38 c = 72.127 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 1.4 69.87 96 0.08 0.037 0.999 12.4 5.5 45248
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 1.4 1.42 93.8 1.616 0.765 0.384 1 5.2 2171
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 1.4 69.87 42998 2224 95.57 0.1415 0.1388 0.1471 0.1936 0.1969 RANDOM 21.966
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] 0.52 -0.16 0.39 -0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_sphericity_free 27.077 r_dihedral_angle_4_deg 20.515 r_sphericity_bonded 15.666 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 6.769 r_rigid_bond_restr 3.917 r_mcangle_it 3.009 r_mcbond_it 2.456 r_mcbond_other 2.418
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.878 r_sphericity_free 27.077 r_dihedral_angle_4_deg 20.515 r_sphericity_bonded 15.666 r_dihedral_angle_3_deg 13.39 r_dihedral_angle_1_deg 6.769 r_rigid_bond_restr 3.917 r_mcangle_it 3.009 r_mcbond_it 2.456 r_mcbond_other 2.418 r_angle_refined_deg 1.835 r_angle_other_deg 1.046 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.01 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 19
Software Software Software Name Purpose Aimless data scaling PHASER phasing REFMAC refinement XDS data reduction