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Tannin acyl hydrolase from Aspergillus niger
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 281 zinc sulfate, polyethylene glycol monomethyl ether 500 and 0.1 M sodium MES at pH 6.5
Crystal Properties Matthews coefficient Solvent content 3.85 68.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 170.92 α = 90 b = 170.92 β = 90 c = 111.061 γ = 120
Symmetry Space Group P 65 2 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 PIXEL DECTRIS EIGER X 16M 2019-03-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 0.9792 Australian Synchrotron MX2
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 1.65 19.76 99.9 0.079 0.023 0.999 20.9 13.4 114035
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 1.65 1.71 1.396 0.384 0.689 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3wmt 1.65 19.76 114035 5698 99.897 0.153 0.1521 0.152 0.1738 0.1738 30.724
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] -0.272 -0.136 -0.272 0.881
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_4_deg 19.133 r_dihedral_angle_3_deg 11.745 r_lrange_it 6.792 r_lrange_other 6.487 r_dihedral_angle_1_deg 6.247 r_scangle_other 5.593 r_scangle_it 5.469 r_scbond_other 3.9 r_scbond_it 3.683
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.105 r_dihedral_angle_4_deg 19.133 r_dihedral_angle_3_deg 11.745 r_lrange_it 6.792 r_lrange_other 6.487 r_dihedral_angle_1_deg 6.247 r_scangle_other 5.593 r_scangle_it 5.469 r_scbond_other 3.9 r_scbond_it 3.683 r_mcangle_it 3.464 r_mcangle_other 3.464 r_angle_other_deg 3.165 r_mcbond_it 2.562 r_mcbond_other 2.562 r_angle_refined_deg 1.88 r_xyhbond_nbd_refined 0.232 r_nbd_refined 0.219 r_symmetry_nbd_other 0.214 r_symmetry_nbd_refined 0.212 r_nbd_other 0.187 r_nbtor_refined 0.178 r_symmetry_xyhbond_nbd_refined 0.146 r_metal_ion_refined 0.123 r_symmetry_metal_ion_refined 0.112 r_symmetry_nbtor_other 0.104 r_chiral_restr 0.096 r_bond_other_d 0.035 r_gen_planes_other 0.019 r_bond_refined_d 0.014 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4280 Nucleic Acid Atoms Solvent Atoms 775 Heterogen Atoms 337
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing