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Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XQ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 3.3M Sodium acetate
Crystal Properties Matthews coefficient Solvent content 3.06 59.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.616 α = 90 b = 171.8 β = 90 c = 342.337 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 CCD RIGAKU JUPITER 210 2016-06-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.0 SPring-8 BL26B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.75 171.17 100 0.087 29.5 7.4 255645
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.8 100 0.353 0.974 6.57 7.5
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 5XQ3 2.75 171.17 242395 12900 99.83 0.19921 0.19583 0.1999 0.26197 0.2609 RANDOM 36.952
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 17.998 r_dihedral_angle_3_deg 15.85 r_dihedral_angle_1_deg 7.16 r_long_range_B_refined 5.493 r_long_range_B_other 5.49 r_scangle_other 3.818 r_mcangle_it 3.808 r_mcangle_other 3.808 r_mcbond_it 2.461
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.267 r_dihedral_angle_4_deg 17.998 r_dihedral_angle_3_deg 15.85 r_dihedral_angle_1_deg 7.16 r_long_range_B_refined 5.493 r_long_range_B_other 5.49 r_scangle_other 3.818 r_mcangle_it 3.808 r_mcangle_other 3.808 r_mcbond_it 2.461 r_mcbond_other 2.46 r_scbond_it 2.432 r_scbond_other 2.432 r_angle_refined_deg 1.683 r_angle_other_deg 1.051 r_chiral_restr 0.097 r_bond_refined_d 0.014 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 56056 Nucleic Acid Atoms Solvent Atoms 746 Heterogen Atoms 239
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing