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endo-alpha-D-arabinanase EndoMA1 from Microbacterium arabinogalactanolyticum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 23% PEG 3350, 0.4 M sodium thiocyanate
Crystal Properties Matthews coefficient Solvent content 2.38 48.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.285 α = 90 b = 128.296 β = 109.38 c = 104.019 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 PILATUS3 S 6M 2017-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.6 46.13 99 0.067 0.041 0.989 9.9 3.8 261209 11.88
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 1.6 1.63 98 0.485 0.356 0.844 1.9
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 1.6 46.18 248219 12950 98.92 0.17867 0.17696 0.1864 0.21121 0.217 RANDOM 17.379
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] -0.88 0.27 1.58 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.231 r_dihedral_angle_2_deg 8.892 r_dihedral_angle_1_deg 7.779 r_long_range_B_refined 4.617 r_long_range_B_other 4.617 r_scangle_other 3.518 r_mcangle_other 2.633 r_mcangle_it 2.632 r_scbond_it 2.589 r_scbond_other 2.589
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.231 r_dihedral_angle_2_deg 8.892 r_dihedral_angle_1_deg 7.779 r_long_range_B_refined 4.617 r_long_range_B_other 4.617 r_scangle_other 3.518 r_mcangle_other 2.633 r_mcangle_it 2.632 r_scbond_it 2.589 r_scbond_other 2.589 r_mcbond_it 2.093 r_mcbond_other 2.091 r_angle_refined_deg 1.906 r_angle_other_deg 0.685 r_chiral_restr 0.101 r_bond_refined_d 0.015 r_gen_planes_refined 0.014 r_bond_other_d 0.001 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 1760 Heterogen Atoms 108
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHENIX phasing