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Crystal structure of glycoside hydrolase family 11 beta-xylanase from Streptomyces olivaceoviridis E-86
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HIX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.4 293 2.9 M sodium chloride, 0.1 M sodium citrate buffer pH 5.4
Crystal Properties Matthews coefficient Solvent content 2.11 41.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.039 α = 90 b = 135.039 β = 90 c = 72.343 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 PIXEL DECTRIS PILATUS3 2M 2018-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
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 2.4 100 100 0.225 10.8 19.3 30040
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 2.4 2.49 1.23 1.7
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1HIX 2.4 49.409 30003 1571 99.983 0.172 0.1678 0.175 0.2449 0.2462 26.848
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] -0.013 -0.006 -0.013 0.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.153 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_4_deg 13.136 r_dihedral_angle_1_deg 9.087 r_lrange_other 5.84 r_lrange_it 5.81 r_scangle_it 4.398 r_scangle_other 4.398 r_mcangle_it 3.863 r_mcangle_other 3.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.153 r_dihedral_angle_3_deg 15.63 r_dihedral_angle_4_deg 13.136 r_dihedral_angle_1_deg 9.087 r_lrange_other 5.84 r_lrange_it 5.81 r_scangle_it 4.398 r_scangle_other 4.398 r_mcangle_it 3.863 r_mcangle_other 3.863 r_scbond_it 3.064 r_scbond_other 3.064 r_mcbond_it 2.694 r_mcbond_other 2.684 r_angle_refined_deg 1.896 r_angle_other_deg 1.395 r_symmetry_xyhbond_nbd_refined 0.224 r_nbd_refined 0.186 r_nbtor_refined 0.186 r_symmetry_nbd_other 0.185 r_nbd_other 0.159 r_xyhbond_nbd_refined 0.144 r_symmetry_nbd_refined 0.11 r_symmetry_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5986 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing