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Structure of Alistipes sp. 3-Keto-2-hydroxy-glucal-hydratase AL2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 0.2 M Magnesium Chloride,
25% PEG 3350,
0.1 M Bis-Tris methane pH 5.5
Crystal Properties Matthews coefficient Solvent content 3.36 63.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.088 α = 90 b = 95.088 β = 90 c = 159.542 γ = 120
Symmetry Space Group P 31 2 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 2023-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 1.18085 CLSI 08B1-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.65 47.54 99.9 0.142 0.15 0.047 0.999 22.9 18.9 24911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.65 2.78 2.057 2.176 0.704 0.868 18.5
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.65 47.54 24670 1229 99.12 0.199 0.1966 0.2441 0.1992 61.222
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] 0.78 0.39 0.78 -2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.301 r_dihedral_angle_2_deg 20.262 r_dihedral_angle_6_deg 15.754 r_lrange_other 13.943 r_lrange_it 13.937 r_scangle_it 13.22 r_scangle_other 13.217 r_scbond_it 10.531 r_scbond_other 10.497 r_mcangle_it 10.367
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 20.301 r_dihedral_angle_2_deg 20.262 r_dihedral_angle_6_deg 15.754 r_lrange_other 13.943 r_lrange_it 13.937 r_scangle_it 13.22 r_scangle_other 13.217 r_scbond_it 10.531 r_scbond_other 10.497 r_mcangle_it 10.367 r_mcangle_other 10.365 r_dihedral_angle_1_deg 8.891 r_mcbond_it 8.552 r_mcbond_other 8.503 r_angle_refined_deg 2.654 r_angle_other_deg 0.878 r_symmetry_nbd_refined 0.275 r_symmetry_nbd_other 0.224 r_nbd_refined 0.212 r_nbtor_refined 0.198 r_nbd_other 0.173 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.116 r_symmetry_nbtor_other 0.1 r_bond_refined_d 0.015 r_gen_planes_refined 0.013 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3938 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PHASER phasing XDS data reduction