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Crystal structure of a beta-helix domain retrieved from capybara gut metagenome
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 20% PEG 6000, 0.1 M sodium acetate pH 5.0, 0,2 M sodium chloride
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.979 α = 90 b = 144.507 β = 90 c = 169.492 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 EIGER X 9M 2018-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.033 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.85 46.38 100 0.129 0.138 0.998 10.37 8.838 85143 39.143
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.96 100 1.8 1.92 0.483 0.97 8.999
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 SAD THROUGHOUT 1.85 46.38 80885 4258 99.93 0.1886 0.1874 0.1977 0.2126 0.2226 RANDOM 47.408
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] 0.23 -0.28 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.832 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_4_deg 12.437 r_dihedral_angle_1_deg 6.696 r_angle_refined_deg 1.264 r_angle_other_deg 0.987 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.832 r_dihedral_angle_3_deg 12.574 r_dihedral_angle_4_deg 12.437 r_dihedral_angle_1_deg 6.696 r_angle_refined_deg 1.264 r_angle_other_deg 0.987 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6422 Nucleic Acid Atoms Solvent Atoms 546 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction SHELXDE phasing