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Endo-deglycosylated hydroxynitrile lyase isozyme 5 mutant L331A from Prunus communis complexed with 2-methyl-4H-benzo[d][1,3]dioxine-6-carbaldehyde
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 8.25 291 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 50.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.519 α = 90 b = 90.968 β = 90 c = 130.493 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 2018-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97918 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 1.6 50 99.4 0.075 0.079 0.024 0.998 8.9 10.5 78057
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 1.6 1.63 99.7 0.854 0.901 0.281 0.853 9.5
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 (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 1.6 33.52 69256 3721 92.88 0.1854 0.18383 0.1948 0.21417 0.2236 RANDOM 14.512
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] -0.16 -0.17 0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.323 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 12.003 r_dihedral_angle_1_deg 7.617 r_long_range_B_refined 4.376 r_long_range_B_other 4.152 r_scangle_other 2.979 r_scbond_it 1.979 r_scbond_other 1.979 r_mcangle_it 1.944
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.323 r_dihedral_angle_4_deg 19.759 r_dihedral_angle_3_deg 12.003 r_dihedral_angle_1_deg 7.617 r_long_range_B_refined 4.376 r_long_range_B_other 4.152 r_scangle_other 2.979 r_scbond_it 1.979 r_scbond_other 1.979 r_mcangle_it 1.944 r_mcangle_other 1.944 r_angle_refined_deg 1.802 r_angle_other_deg 1.468 r_mcbond_it 1.296 r_mcbond_other 1.296 r_chiral_restr 0.088 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 3952 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 161
Software Software Software Name Purpose REFMAC refinement HKL-3000 data scaling HKL-3000 data reduction PHASER phasing