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Polygalacturonate Lyase by Fusing with a Self-assembling Amphipathic Peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1BN8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 7.5 293 0.2 M sodium bromide, 20 mM Glycine-NaOH, 20 % polyethylene glycol 3350, 7 mM calcium chloride, 20 % glycerol
Crystal Properties Matthews coefficient Solvent content 2.2 44.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.094 α = 67.51 b = 51.212 β = 74.93 c = 51.296 γ = 78.75
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RIGAKU SATURN 944 2015-12-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL3 1.54 SACLA BL3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.86 28.427 91.8 12.1 2.3 18202
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 FOURIER SYNTHESIS THROUGHOUT 1BN8 2.05 28.427 18202 1051 83 0.17709 0.17581 0.1847 0.19952 0.2078 RANDOM 23.746
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] -1.62 0.39 0.31 -0.26 -0.73 1.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.694 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 14.087 r_dihedral_angle_1_deg 7.291 r_long_range_B_refined 5.268 r_long_range_B_other 5.198 r_scangle_other 3.818 r_mcangle_it 2.677 r_mcangle_other 2.677 r_scbond_it 2.661
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.694 r_dihedral_angle_4_deg 16.247 r_dihedral_angle_3_deg 14.087 r_dihedral_angle_1_deg 7.291 r_long_range_B_refined 5.268 r_long_range_B_other 5.198 r_scangle_other 3.818 r_mcangle_it 2.677 r_mcangle_other 2.677 r_scbond_it 2.661 r_scbond_other 2.659 r_mcbond_it 1.961 r_mcbond_other 1.961 r_angle_refined_deg 1.703 r_angle_other_deg 0.954 r_chiral_restr 0.117 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 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 3066 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement