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Family S1_16 sulfatase from metagenomic dataset AMOR
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, HANGING DROP 5 293 0.1M Sodium citrate pH 5.0, 12% PEG 3350
Crystal Properties Matthews coefficient Solvent content 6.87 82.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 206.314 α = 90 b = 206.314 β = 90 c = 206.314 γ = 90
Symmetry Space Group I 21 3
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 2022-02-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.98011 SOLEIL PROXIMA 2
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 3.11 48.6 100 0.6 0.132 0.996 11.4 42.1 26345
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.11 3.33 99.5 0.94 0.53
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 (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 3.11 45.89 25055 1270 99.91 0.16331 0.16184 0.1755 0.19249 0.1971 RANDOM 74.526
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.354 r_dihedral_angle_4_deg 20.442 r_dihedral_angle_3_deg 19.233 r_long_range_B_refined 14.227 r_long_range_B_other 14.227 r_scangle_other 12.025 r_mcangle_it 9.775 r_mcangle_other 9.773 r_scbond_it 8.585 r_scbond_other 8.583
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.354 r_dihedral_angle_4_deg 20.442 r_dihedral_angle_3_deg 19.233 r_long_range_B_refined 14.227 r_long_range_B_other 14.227 r_scangle_other 12.025 r_mcangle_it 9.775 r_mcangle_other 9.773 r_scbond_it 8.585 r_scbond_other 8.583 r_dihedral_angle_1_deg 8.189 r_mcbond_it 7.128 r_mcbond_other 7.019 r_angle_refined_deg 1.873 r_angle_other_deg 1.389 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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 3601 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing