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C-terminal peptide depleted mutant of hydroxynitrile lyase from Passiflora edulis (PeHNL)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XZQ
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 = 85.494 α = 90 b = 87.83 β = 105.23 c = 104.578 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 2015-11-19 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 1.8 100.91 98.4 0.058 0.064 0.027 0.027 0.999 18.3 5.3 135702
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 97.3 0.394 0.435 0.182 0.182 0.911 4.7 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 THROUGHOUT 5XZQ 1.8 100.91 128976 6702 98.24 0.1738 0.17249 0.1806 0.19871 0.2066 RANDOM 22.81
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] 0.55 -0.09 0.48 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.192 r_dihedral_angle_4_deg 14.403 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 5.399 r_long_range_B_other 4.993 r_scangle_other 2.197 r_mcangle_it 2.104 r_mcangle_other 2.104 r_angle_refined_deg 1.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.192 r_dihedral_angle_4_deg 14.403 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_1_deg 6.164 r_long_range_B_refined 5.399 r_long_range_B_other 4.993 r_scangle_other 2.197 r_mcangle_it 2.104 r_mcangle_other 2.104 r_angle_refined_deg 1.305 r_scbond_it 1.297 r_scbond_other 1.297 r_mcbond_it 1.219 r_mcbond_other 1.218 r_angle_other_deg 0.894 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 10329 Nucleic Acid Atoms Solvent Atoms 1743 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling MOLREP phasing