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DE NOVO designed zinc hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model Other de novo designed model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 20% (w/v) PEG 3000, 100 mM Imidazole/ Hydrochloric acid pH 8.0, 200 mM Zinc acetate
Crystal Properties Matthews coefficient Solvent content 2.32 46.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.874 α = 90 b = 53.874 β = 90 c = 78.021 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 181 PIXEL RIGAKU HyPix-6000HE 2024-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE Cu FINE FOCUS 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.3 29.93 95.35 0.1926 0.2039 0.0658 0.988 27.58 9.5 6153 17.33
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.382 99.67 0.3467 0.366 0.1152 0.781 12.78 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 29.93 0.15 5871 584 95.4 0.2472 0.2464 0.3033 0.3017
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 3.321 f_angle_d 0.356 f_chiral_restr 0.03 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 985 Nucleic Acid Atoms Solvent Atoms 80 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement PDB_EXTRACT data extraction PHENIX model building Coot model building PHASER phasing XDS data reduction HKL-2000 data scaling