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GH42 alpha-L-arabinopyranosidase from Bifidobacterium animalis subsp. lactis Bl-04
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KWG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 12% glycerol, 1.6 M ammonium sulfate, 0.1 M MES buffer pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.11 60.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.954 α = 90 b = 177.954 β = 90 c = 375.697 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2014-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 50 100 0.127 27.7 14.9 400874
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.03 100 0.502 0.989 3.8 14.6
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 1KWG 2 49.368 380693 20004 99.96 0.15704 0.15525 0.1649 0.19127 0.1971 RANDOM 26.94
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] -0.37 -0.37 0.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.772 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_1_deg 6.789 r_long_range_B_refined 5.761 r_long_range_B_other 5.761 r_scangle_other 4.634 r_angle_other_deg 3.704 r_scbond_it 3.338 r_scbond_other 3.331
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.465 r_dihedral_angle_4_deg 17.772 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_1_deg 6.789 r_long_range_B_refined 5.761 r_long_range_B_other 5.761 r_scangle_other 4.634 r_angle_other_deg 3.704 r_scbond_it 3.338 r_scbond_other 3.331 r_mcangle_it 2.874 r_mcangle_other 2.874 r_mcbond_it 2.344 r_mcbond_other 2.344 r_angle_refined_deg 1.972 r_chiral_restr 0.129 r_gen_planes_other 0.023 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 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 32478 Nucleic Acid Atoms Solvent Atoms 2528 Heterogen Atoms 410
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling BALBES phasing