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C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL) bound with (R)-mandelonitrile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XZT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 21% (w/v) PEG3350
2.1% (w/v) 1,6-hexanediol
150 mM NaCl
50 mM HEPES-NaOH, pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.56 51.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.811 α = 90 b = 88.494 β = 105.07 c = 104.454 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 100 PIXEL DECTRIS PILATUS3 2M 2015-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.10 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 49.12 97.2 0.064 0.071 0.03 0.03 0.999 15.4 5.4 135483
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 95.6 0.546 0.603 0.254 0.254 0.863 3.1 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 FREE R-VALUE 5XZT 1.8 49.12 128774 6683 97.03 0.18253 0.18088 0.1882 0.21477 0.2201 RANDOM 27.468
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] 1.37 0.1 -0.07 -1.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.856 r_dihedral_angle_4_deg 14.126 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.246 r_long_range_B_refined 5.498 r_long_range_B_other 5.207 r_scangle_other 2.94 r_mcangle_it 2.663 r_mcangle_other 2.663 r_scbond_it 1.773
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.856 r_dihedral_angle_4_deg 14.126 r_dihedral_angle_3_deg 13.69 r_dihedral_angle_1_deg 6.246 r_long_range_B_refined 5.498 r_long_range_B_other 5.207 r_scangle_other 2.94 r_mcangle_it 2.663 r_mcangle_other 2.663 r_scbond_it 1.773 r_scbond_other 1.772 r_mcbond_it 1.601 r_mcbond_other 1.599 r_angle_refined_deg 1.326 r_angle_other_deg 0.891 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 10303 Nucleic Acid Atoms Solvent Atoms 1446 Heterogen Atoms 128
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing