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Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A/S333V/P340L from Prunus communis complexed with 2,2-dimethyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde (noncatalytic conformation)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 tris-bicine, 100 mM, pH 8.5; CaCl2, 60 mM; MgCl2, 60 mM; PEG 500MME, 20%, v/v; PEG 20000, 10%, w/v
Crystal Properties Matthews coefficient Solvent content 2.49 50.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.519 α = 90 b = 90.844 β = 90 c = 130.692 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2020-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97892 SSRF BL19U1
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 1.8 50 100 0.061 0.066 0.026 0.989 8.3 6.5 55484
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 1.8 1.83 100 0.264 0.289 0.116 0.966 6.1
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-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 1.8 46.35 52467 2773 99.47 0.154 0.15364 0.15189 0.1639 0.18735 0.1947 RANDOM 19.567
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] -0.08 -0.18 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 12.008 r_dihedral_angle_1_deg 7.371 r_long_range_B_refined 6.088 r_long_range_B_other 5.692 r_scangle_other 4.206 r_scbond_it 2.907 r_scbond_other 2.797 r_mcangle_it 2.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.915 r_dihedral_angle_4_deg 18.107 r_dihedral_angle_3_deg 12.008 r_dihedral_angle_1_deg 7.371 r_long_range_B_refined 6.088 r_long_range_B_other 5.692 r_scangle_other 4.206 r_scbond_it 2.907 r_scbond_other 2.797 r_mcangle_it 2.331 r_mcangle_other 2.33 r_angle_refined_deg 1.793 r_mcbond_it 1.752 r_mcbond_other 1.752 r_angle_other_deg 1.466 r_chiral_restr 0.093 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3917 Nucleic Acid Atoms Solvent Atoms 535 Heterogen Atoms 187
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing