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Native crystal structure of a GH39 beta-xylosidase XynB1 from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PX8 PDB ENTRY 1PX8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM HEPES PH 7.5, 50 MM NACL, 20% (W/V) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.57 52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.668 α = 90 b = 165.744 β = 90 c = 311.004 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 CCD ADSC CCD 2002-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.1 24.9 98.2 0.16 8 3.7 273112
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.2 98.2 0.44 2.4 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1PX8 2.2 50 225867 11944 98 0.211 0.209 0.259 0.2337 RANDOM 17.34
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] 0.93 -1.02 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.913 r_scangle_it 2.553 r_scbond_it 1.549 r_angle_refined_deg 1.403 r_mcangle_it 0.965 r_angle_other_deg 0.858 r_mcbond_it 0.514 r_symmetry_vdw_other 0.282 r_nbd_other 0.233 r_symmetry_vdw_refined 0.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.913 r_scangle_it 2.553 r_scbond_it 1.549 r_angle_refined_deg 1.403 r_mcangle_it 0.965 r_angle_other_deg 0.858 r_mcbond_it 0.514 r_symmetry_vdw_other 0.282 r_nbd_other 0.233 r_symmetry_vdw_refined 0.209 r_nbd_refined 0.203 r_symmetry_hbond_refined 0.17 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.09 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_other 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 32725 Nucleic Acid Atoms Solvent Atoms 1367 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing