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GH3 exo-beta-xylosidase (XlnD)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5A7M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 Halogens NaF; NaBr; NaI, imidazole/MES pH 6.5, PEG550/PEG20K.
Crystal Properties Matthews coefficient Solvent content 2.28 46.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.47 α = 90 b = 90.58 β = 90 c = 244.37 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 PILATUS 6M-F 2017-07-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.979500 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.48 33.24 100 0.037 0.999 10.5 8.1 260021
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 1.48 1.51 0.485 1
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 (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 5A7M 1.48 33.24 246999 13022 99.94 0.16076 0.15906 0.1624 0.19313 0.1962 RANDOM 21.022
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] -1.47 1.99 -0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_4_deg 17.341 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 4.467 r_long_range_B_other 4.466 r_scangle_other 3.554 r_scbond_it 2.517 r_scbond_other 2.517 r_mcangle_other 2.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.459 r_dihedral_angle_4_deg 17.341 r_dihedral_angle_3_deg 11.721 r_dihedral_angle_1_deg 7.072 r_long_range_B_refined 4.467 r_long_range_B_other 4.466 r_scangle_other 3.554 r_scbond_it 2.517 r_scbond_other 2.517 r_mcangle_other 2.121 r_mcangle_it 2.12 r_angle_refined_deg 1.842 r_mcbond_it 1.628 r_mcbond_other 1.623 r_angle_other_deg 1.544 r_chiral_restr 0.097 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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 11778 Nucleic Acid Atoms Solvent Atoms 1821 Heterogen Atoms 585
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing