☰ Navigation Tabs
Crystal structure of non-specific endoxylanase from Acetivibrio clariflavus (AcXyn30B), that belongs to subfamily GH30_12.
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 8.5 293 Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Potassium sodium tartrate tetrahydrate, Sodium oxamate, Tris (base), BICINE, MPD, PEG 1000, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.598 α = 90 b = 72.945 β = 90 c = 90.922 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 16M 2024-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX IV BEAMLINE BioMAX 0.729 MAX IV BioMAX
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 1.14 48.36 100 0.091 0.099 0.037 0.997 15.1 13.4 156623
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 1.14 1.16 99.9 0.555 0.6 0.226 0.934 4 13.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.14 48.36 156457 7769 99.948 0.155 0.1539 0.1525 0.1693 0.1682 14.159
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] -0.129 0.307 -0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.747 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_2_deg 7.801 r_dihedral_angle_1_deg 6.985 r_lrange_it 4.447 r_lrange_other 4.27 r_scangle_it 2.531 r_scangle_other 2.531 r_angle_refined_deg 1.968 r_scbond_it 1.698
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.747 r_dihedral_angle_3_deg 11.609 r_dihedral_angle_2_deg 7.801 r_dihedral_angle_1_deg 6.985 r_lrange_it 4.447 r_lrange_other 4.27 r_scangle_it 2.531 r_scangle_other 2.531 r_angle_refined_deg 1.968 r_scbond_it 1.698 r_scbond_other 1.698 r_mcangle_other 1.249 r_mcangle_it 1.246 r_mcbond_it 0.888 r_mcbond_other 0.871 r_angle_other_deg 0.685 r_nbd_refined 0.222 r_symmetry_nbd_refined 0.217 r_nbtor_refined 0.193 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.164 r_nbd_other 0.162 r_symmetry_xyhbond_nbd_other 0.156 r_chiral_restr 0.102 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.014 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3357 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PHASER phasing Aimless data scaling XDS data reduction