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Structure of GH43 family enzyme, Xylan 1, 4 Beta- xylosidase from pseudopedobacter saltans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NOV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293.15 18% PEG 3350, 5% PROPANOL, 0.15M IMIDAZOLE
Crystal Properties Matthews coefficient Solvent content 2.14 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.34 α = 102.734 b = 89.662 β = 93.985 c = 138.437 γ = 98.237
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 273 PIXEL DECTRIS PILATUS3 2M 2022-07-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.96546 ESRF BM30A
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 2.5 134.29 95 0.08 0.1 0.07 0.94 0.04 1.92 103346 30.2
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 2.5 2.56 97 0.02 0.28 0.19 0.93 2.01
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 4NOV 2.566 134.29 103343 5180 95.375 0.166 0.1634 0.1672 0.2091 0.1761 33.093
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] 2.558 1.763 0.582 -0.804 0.843 -2.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.327 r_dihedral_angle_6_deg 17.669 r_lrange_it 10.506 r_scangle_it 7.745 r_dihedral_angle_1_deg 6.808 r_mcangle_it 6.384 r_scbond_it 5.791 r_dihedral_angle_2_deg 4.871 r_mcbond_it 4.519 r_angle_refined_deg 1.494
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 19.327 r_dihedral_angle_6_deg 17.669 r_lrange_it 10.506 r_scangle_it 7.745 r_dihedral_angle_1_deg 6.808 r_mcangle_it 6.384 r_scbond_it 5.791 r_dihedral_angle_2_deg 4.871 r_mcbond_it 4.519 r_angle_refined_deg 1.494 r_nbtor_refined 0.319 r_nbd_refined 0.206 r_symmetry_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.187 r_metal_ion_refined 0.181 r_xyhbond_nbd_refined 0.164 r_ncsr_local_group_18 0.126 r_ncsr_local_group_23 0.126 r_ncsr_local_group_27 0.125 r_ncsr_local_group_13 0.124 r_ncsr_local_group_14 0.124 r_ncsr_local_group_20 0.124 r_ncsr_local_group_22 0.124 r_ncsr_local_group_25 0.124 r_ncsr_local_group_6 0.123 r_ncsr_local_group_9 0.123 r_ncsr_local_group_19 0.123 r_ncsr_local_group_21 0.123 r_ncsr_local_group_26 0.123 r_ncsr_local_group_28 0.123 r_ncsr_local_group_11 0.122 r_ncsr_local_group_3 0.121 r_ncsr_local_group_4 0.121 r_ncsr_local_group_5 0.121 r_ncsr_local_group_2 0.12 r_ncsr_local_group_7 0.12 r_ncsr_local_group_16 0.12 r_ncsr_local_group_1 0.118 r_ncsr_local_group_10 0.118 r_ncsr_local_group_12 0.118 r_ncsr_local_group_24 0.118 r_ncsr_local_group_15 0.115 r_ncsr_local_group_17 0.113 r_ncsr_local_group_8 0.111 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27430 Nucleic Acid Atoms Solvent Atoms 1325 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement Coot model building iMOSFLM data reduction Aimless data scaling PHASER phasing