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Crystal structure of Pseudopedobacter saltans GH43 beta-xylosidase in complex with xylose.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8HCJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 5% propanol, 0.1M imidazole and 14% PEG 3550.
Crystal Properties Matthews coefficient Solvent content 2.45 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.585 α = 102.818 b = 89.435 β = 94.019 c = 138.443 γ = 97.882
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 EIGER2 S 9M 2023-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
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 2.8 47.842 93 0.17 0.24 0.9 4 1.8 78398 21.44
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.87 94 0.37 0.37 0.52 0.72 2 1.8
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 8HCJ 2.8 47.841 77725 3966 93.048 0.221 0.2183 0.2267 0.2728 0.2828 23.778
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] 0.9 -0.01 2.517 -1.118 0.451 -0.444
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.128 r_dihedral_angle_6_deg 13.996 r_dihedral_angle_2_deg 12.352 r_dihedral_angle_1_deg 7.852 r_lrange_it 6.638 r_scangle_it 4.99 r_mcangle_it 3.791 r_scbond_it 3.303 r_mcbond_it 2.351 r_angle_refined_deg 2.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.128 r_dihedral_angle_6_deg 13.996 r_dihedral_angle_2_deg 12.352 r_dihedral_angle_1_deg 7.852 r_lrange_it 6.638 r_scangle_it 4.99 r_mcangle_it 3.791 r_scbond_it 3.303 r_mcbond_it 2.351 r_angle_refined_deg 2.317 r_nbtor_refined 0.315 r_symmetry_nbd_refined 0.254 r_nbd_refined 0.222 r_metal_ion_refined 0.192 r_chiral_restr 0.149 r_xyhbond_nbd_refined 0.148 r_symmetry_xyhbond_nbd_refined 0.112 r_ncsr_local_group_1 0.103 r_ncsr_local_group_8 0.101 r_ncsr_local_group_4 0.099 r_ncsr_local_group_9 0.099 r_ncsr_local_group_13 0.099 r_ncsr_local_group_17 0.099 r_ncsr_local_group_26 0.099 r_ncsr_local_group_6 0.098 r_ncsr_local_group_11 0.098 r_ncsr_local_group_28 0.098 r_ncsr_local_group_2 0.097 r_ncsr_local_group_3 0.097 r_ncsr_local_group_5 0.097 r_ncsr_local_group_7 0.097 r_ncsr_local_group_10 0.097 r_ncsr_local_group_24 0.096 r_ncsr_local_group_12 0.095 r_ncsr_local_group_14 0.095 r_ncsr_local_group_23 0.095 r_ncsr_local_group_15 0.094 r_ncsr_local_group_27 0.094 r_ncsr_local_group_20 0.093 r_ncsr_local_group_16 0.091 r_ncsr_local_group_21 0.091 r_ncsr_local_group_18 0.09 r_ncsr_local_group_19 0.089 r_ncsr_local_group_22 0.089 r_ncsr_local_group_25 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27396 Nucleic Acid Atoms Solvent Atoms 244 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing