☰ Navigation Tabs
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 2.09 41.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.23 α = 90 b = 41.544 β = 104.11 c = 72.13 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 69.96 85.6 0.105 0.052 0.997 9.5 5 27511
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 45 1.078 0.554 0.431 1.3 4.5 704
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 69.96 26057 1441 85.2 0.1871 0.1846 0.1956 0.2296 0.2355 RANDOM 23.532
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] 0.21 0.75 -0.93 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_4_deg 21.906 r_dihedral_angle_3_deg 14.643 r_dihedral_angle_1_deg 11.753 r_mcangle_it 3.079 r_mcbond_it 2.087 r_mcbond_other 2.052 r_angle_refined_deg 1.879 r_angle_other_deg 1.023 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.952 r_dihedral_angle_4_deg 21.906 r_dihedral_angle_3_deg 14.643 r_dihedral_angle_1_deg 11.753 r_mcangle_it 3.079 r_mcbond_it 2.087 r_mcbond_other 2.052 r_angle_refined_deg 1.879 r_angle_other_deg 1.023 r_chiral_restr 0.107 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2059 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction