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INCYPRO crosslinked dimer of the D-stereospecific hydrolase dHy1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Unpublished structure of APO DHy
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293.15 100 mM MES/Imidazole pH 7, 13 %(v/v) PEG-20000, 26 %(w/v) PEG550-MME, 0.1 M Morpheus Carboxylic Acids
Crystal Properties Matthews coefficient Solvent content 2.08 40.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.776 α = 75.692 b = 53.764 β = 75.693 c = 57.373 γ = 87.81
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 EIGER2 XE 16M 2024-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.771 43.115 91.8 0.034 0.999 11.8 6.9 35659 1.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.771 1.967 56.7 0.509 0.49 1.4 6.6
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-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.771 43.115 35658 1752 60.746 0.241 0.2399 0.2427 0.2696 0.273 43.221
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] 25.97 -6.572 -6.465 -20.958 6.185 -5.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.814 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_6_deg 11.552 r_dihedral_angle_1_deg 6.741 r_lrange_it 3.142 r_lrange_other 3.132 r_mcangle_it 1.553 r_mcangle_other 1.553 r_dihedral_angle_other_2_deg 1.254 r_scangle_it 1.049
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.814 r_dihedral_angle_3_deg 12.582 r_dihedral_angle_6_deg 11.552 r_dihedral_angle_1_deg 6.741 r_lrange_it 3.142 r_lrange_other 3.132 r_mcangle_it 1.553 r_mcangle_other 1.553 r_dihedral_angle_other_2_deg 1.254 r_scangle_it 1.049 r_scangle_other 1.049 r_angle_refined_deg 0.886 r_mcbond_it 0.835 r_mcbond_other 0.835 r_scbond_it 0.532 r_scbond_other 0.532 r_angle_other_deg 0.347 r_symmetry_xyhbond_nbd_refined 0.176 r_symmetry_nbd_other 0.175 r_nbd_refined 0.173 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.155 r_nbd_other 0.122 r_symmetry_nbd_refined 0.095 r_symmetry_nbtor_other 0.074 r_chiral_restr 0.044 r_ncsr_local_group_1 0.026 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5194 Nucleic Acid Atoms Solvent Atoms 157 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction autoPROC data scaling PHASER phasing Coot model building