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Niako3494, a bacterial protein structure in glycoside hydrolase family 20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold Alphafold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL drop size, +50 nL 1:10000 diluted seed stock. Cryoprotectant used was made up with 20% PEG400 in 80% mother liquor.
Crystal Properties Matthews coefficient Solvent content 3 58.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 146.987 α = 90 b = 254.589 β = 90 c = 139.58 γ = 90
Symmetry Space Group C 2 2 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 EIGER2 XE 16M 2022-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.27 73.49 99.9 0.958 6.3 13.9 120442
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.27 2.31 99.1 0.336 1.1 13.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Alphafold 2.27 73.49 120411 6125 99.939 0.287 0.2828 0.2483 0.3561 0.3099 31.39
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] 6.14 7.703 -13.844
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.057 r_dihedral_angle_6_deg 14.829 r_dihedral_angle_1_deg 11.394 r_dihedral_angle_2_deg 10.329 r_lrange_it 5.836 r_lrange_other 5.836 r_mcangle_it 4.12 r_mcangle_other 4.12 r_scangle_it 3.202 r_scangle_other 3.202
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.057 r_dihedral_angle_6_deg 14.829 r_dihedral_angle_1_deg 11.394 r_dihedral_angle_2_deg 10.329 r_lrange_it 5.836 r_lrange_other 5.836 r_mcangle_it 4.12 r_mcangle_other 4.12 r_scangle_it 3.202 r_scangle_other 3.202 r_mcbond_it 2.802 r_mcbond_other 2.802 r_scbond_it 2.176 r_scbond_other 2.176 r_angle_refined_deg 1.613 r_angle_other_deg 0.515 r_symmetry_xyhbond_nbd_refined 0.347 r_metal_ion_refined 0.342 r_xyhbond_nbd_refined 0.29 r_nbd_refined 0.288 r_symmetry_nbd_refined 0.237 r_symmetry_nbd_other 0.234 r_xyhbond_nbd_other 0.203 r_nbd_other 0.201 r_nbtor_refined 0.198 r_symmetry_xyhbond_nbd_other 0.106 r_symmetry_nbtor_other 0.088 r_chiral_restr 0.071 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13710 Nucleic Acid Atoms Solvent Atoms 28 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling MOLREP phasing