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endo-alpha-D-arabinanase EndoMA1 D51N mutant from Microbacterium arabinogalactanolyticum in complex with arabinooligosaccharides
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 303.15 0.12 M MES-NaOH (pH 6.0), 5% PEG3000, 20% PEG200, 5 mM arabinononaose with acetonide tag
Crystal Properties Matthews coefficient Solvent content 2.73 54.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.708 α = 90 b = 137.731 β = 90 c = 148.589 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 PIXEL DECTRIS PILATUS 2M-F 2021-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 46.65 100 0.114 0.047 0.625 12 6.7 217228 20.21
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.83 1.235 0.528 0.625 2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.8 46.65 206113 10991 99.97 0.16074 0.15917 0.19049 0.1937 RANDOM 22.115
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] 0.05 -0.52 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.03 r_dihedral_angle_2_deg 8.743 r_dihedral_angle_1_deg 7.353 r_long_range_B_other 5.357 r_long_range_B_refined 5.356 r_scangle_other 4.293 r_scbond_it 2.935 r_scbond_other 2.935 r_mcangle_it 2.52 r_mcangle_other 2.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.03 r_dihedral_angle_2_deg 8.743 r_dihedral_angle_1_deg 7.353 r_long_range_B_other 5.357 r_long_range_B_refined 5.356 r_scangle_other 4.293 r_scbond_it 2.935 r_scbond_other 2.935 r_mcangle_it 2.52 r_mcangle_other 2.52 r_mcbond_it 1.994 r_mcbond_other 1.994 r_angle_refined_deg 1.581 r_angle_other_deg 0.566 r_chiral_restr 0.08 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.003 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 14836 Nucleic Acid Atoms Solvent Atoms 1314 Heterogen Atoms 424
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing