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Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 2.9 M Sodium Acetate
Crystal Properties Matthews coefficient Solvent content 3 58.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 167.471 α = 90 b = 167.471 β = 90 c = 172.289 γ = 90
Symmetry Space Group P 42 21 2
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 RAYONIX MX-225 2015-10-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 0.979 SPring-8 BL26B2
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 2.85 120.09 100 0.117 33 20 57725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.85 2.9 100 0.886 3 15
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.85 120.09 54481 1956 97.82 0.17329 0.17103 0.1754 0.23656 0.2359 RANDOM 60.539
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 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_3_deg 17.257 r_dihedral_angle_4_deg 17.095 r_long_range_B_other 8.322 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 7.475 r_scangle_other 6.307 r_mcangle_it 6.13 r_mcangle_other 6.13 r_scbond_it 4.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.739 r_dihedral_angle_3_deg 17.257 r_dihedral_angle_4_deg 17.095 r_long_range_B_other 8.322 r_long_range_B_refined 8.321 r_dihedral_angle_1_deg 7.475 r_scangle_other 6.307 r_mcangle_it 6.13 r_mcangle_other 6.13 r_scbond_it 4.137 r_scbond_other 4.136 r_mcbond_it 4.134 r_mcbond_other 4.127 r_angle_refined_deg 1.637 r_angle_other_deg 1.037 r_chiral_restr 0.093 r_bond_refined_d 0.013 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 13912 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing