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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 LIQUID DIFFUSION 8 291 2.5 M NaCl;
95 mM IMD-HCl pH8.0;
200 mM ZnAc
Crystal Properties Matthews coefficient Solvent content 2.03 39.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.817 α = 90 b = 52.647 β = 91.34 c = 142.325 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 181 PIXEL RIGAKU HyPix-6000HE 2025-05-15 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 2.73 26.24 95.18 0.181 0.217 0.1174 0.982 7.83 9.16 23460
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 2.73 2.828 95.64 0.3837 0.4541 0.2384 0.835 3.54
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.73 26.24 22792 1174 95.6 0.2993 0.3015 0.311 0.3128
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 7.359 f_angle_d 0.962 f_chiral_restr 0.046 f_bond_d 0.004 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7505 Nucleic Acid Atoms Solvent Atoms 47 Heterogen Atoms 5
Software Software Software Name Purpose PHENIX refinement XDS data reduction HKL-2000 data scaling PHENIX phasing PHENIX model building