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Diels-Alderase AbyU mutant - Y76F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DYV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.25 M Magnesium Chloride
0.1M HEPES
10% PEG 6K
Crystal Properties Matthews coefficient Solvent content 2.25 45.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.71 α = 90.11 b = 53.82 β = 96.98 c = 60.48 γ = 94.66
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 193 PIXEL DECTRIS EIGER2 XE 16M 2019-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim I (All) 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 1.56 40.58 95.5 0.033 11.3 3.5 84307
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 0.7
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 1.56 40.577 84306 4233 95.462 0.174 0.1724 0.1698 0.2079 0.2036 36.42
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] 2.576 -0.799 0.12 -2.337 -0.487 -0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.153 r_dihedral_angle_3_deg 12.775 r_lrange_other 10.504 r_lrange_it 10.48 r_scangle_it 8.542 r_scangle_other 8.541 r_dihedral_angle_2_deg 8.147 r_dihedral_angle_1_deg 6.885 r_scbond_it 5.901 r_scbond_other 5.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 18.153 r_dihedral_angle_3_deg 12.775 r_lrange_other 10.504 r_lrange_it 10.48 r_scangle_it 8.542 r_scangle_other 8.541 r_dihedral_angle_2_deg 8.147 r_dihedral_angle_1_deg 6.885 r_scbond_it 5.901 r_scbond_other 5.861 r_mcangle_other 5.86 r_mcangle_it 5.859 r_mcbond_it 4.316 r_mcbond_other 4.312 r_angle_refined_deg 1.915 r_angle_other_deg 0.654 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.206 r_symmetry_nbd_other 0.201 r_symmetry_xyhbond_nbd_refined 0.192 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.121 r_symmetry_xyhbond_nbd_other 0.107 r_chiral_restr 0.101 r_nbd_other 0.098 r_symmetry_nbtor_other 0.091 r_chiral_restr_other 0.024 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4120 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing