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Crystal structure of xylanase from Streptomyces olivaceoviridis E-86 complexed with xylotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XYF PDB ENTRY 1XYF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 298 ammonium sulfate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.63 53.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.37 α = 90 b = 94.46 β = 90 c = 138.27 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 IMAGE PLATE RIGAKU RAXIS IV 2001-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
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 36.3 86.8 0.063 21.3 5.43 67459 345176 2 2 18.1
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) 2 2.07 77.4 0.285 7.1 4.68 6642
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 PDB ENTRY 1XYF 2.1 29.82 51446 51446 5211 88.2 0.189 0.189 0.189 0.2018 0.24 0.2475 RANDOM
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] 1.21 -0.55 -0.65
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.41 c_mcangle_it 1.93 c_scbond_it 1.78 c_angle_deg 1.3 c_mcbond_it 1.25 c_improper_angle_d 0.69 c_bond_d 0.005 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 23 c_scangle_it 2.41 c_mcangle_it 1.93 c_scbond_it 1.78 c_angle_deg 1.3 c_mcbond_it 1.25 c_improper_angle_d 0.69 c_bond_d 0.005 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6595 Nucleic Acid Atoms Solvent Atoms 806 Heterogen Atoms 161
Software Software Software Name Purpose CrystalClear data collection CrystalClear data reduction CNS refinement CrystalClear data scaling CNS phasing