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Alpha-L-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WVS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 291.15 25% (w/v) PEG 3350,
0.2 M Ammonium acetate,
0.1 M BIS-TRIS buffer,
Additive: 50 mM Maltose
Crystal Properties Matthews coefficient Solvent content 2.54 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.772 α = 90 b = 148.758 β = 90 c = 194.895 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 6M-F 2015-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9201 PETRA III, EMBL c/o DESY P13 (MX1)
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 2.2 48.93 99.4 0.099 12.3 5 157780 -3.7 24.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.24 99.2 0.709 2.1 4.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2WVS 2.2 48.93 157724 7763 99.2 0.169 0.167 0.217 0.1711 RANDOM SELECTION 33.97
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] -0.99 0.29 0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_3_deg 15.301 r_long_range_B_refined 7.667 r_long_range_B_other 7.667 r_dihedral_angle_1_deg 6.786 r_scangle_other 6.367 r_scbond_it 4.228 r_scbond_other 4.226 r_mcangle_it 4.173
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.562 r_dihedral_angle_4_deg 19.314 r_dihedral_angle_3_deg 15.301 r_long_range_B_refined 7.667 r_long_range_B_other 7.667 r_dihedral_angle_1_deg 6.786 r_scangle_other 6.367 r_scbond_it 4.228 r_scbond_other 4.226 r_mcangle_it 4.173 r_mcangle_other 4.173 r_mcbond_it 2.958 r_mcbond_other 2.958 r_angle_refined_deg 1.825 r_angle_other_deg 1.181 r_chiral_restr 0.101 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.005 r_bond_other_d 0.001 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 20508 Nucleic Acid Atoms Solvent Atoms 1392 Heterogen Atoms 455
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing