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Hydroxynitrile lyase from Passiflora edulis (PeHNL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SI9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% (w/v) PEG6000
200 mM lithium acetate
100 mM Bis-Tris-HCl, pH 6.5
Crystal Properties Matthews coefficient Solvent content 1.93 35.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.446 α = 90 b = 88.567 β = 105.99 c = 104.574 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 PILATUS 2M 2015-06-20 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) 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 2.8 100.53 99.3 0.044 0.048 0.021 0.999 19.2 5.3 196401
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.95 99 0.197 0.217 0.089 0.986 7.7 5.6
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 THROUGHOUT 1SI9 2.8 100.53 34927 1892 99.11 0.21127 0.20748 0.2131 0.27877 0.2768 RANDOM 63.358
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] 2.61 1.39 3.67 -6.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.372 r_dihedral_angle_3_deg 19.482 r_dihedral_angle_4_deg 15.009 r_long_range_B_refined 9.119 r_long_range_B_other 9.119 r_dihedral_angle_1_deg 8.264 r_mcangle_it 6.69 r_mcangle_other 6.689 r_scangle_other 5.972 r_mcbond_it 4.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.372 r_dihedral_angle_3_deg 19.482 r_dihedral_angle_4_deg 15.009 r_long_range_B_refined 9.119 r_long_range_B_other 9.119 r_dihedral_angle_1_deg 8.264 r_mcangle_it 6.69 r_mcangle_other 6.689 r_scangle_other 5.972 r_mcbond_it 4.216 r_mcbond_other 4.213 r_scbond_it 3.704 r_scbond_other 3.704 r_angle_refined_deg 1.581 r_angle_other_deg 1.023 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 10523 Nucleic Acid Atoms Solvent Atoms 63 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing