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Xylanase Xyn10a from Streptomyces lividans in complex with xylobio-isofagomine at pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OD8 PDB ENTRY 1OD8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100 MM IMIDAZOLE, PH 7.5 16% PEG 5K MME, 5% ISOPROPANOL
Crystal Properties Matthews coefficient Solvent content 2 36.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.328 α = 90 b = 46.132 β = 90 c = 86.382 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 TOROIDAL MIRROR 2003-12-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.1 23 95.1 0.056 15.6 5.3 97030
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 1.1 1.16 70.4 0.217 4.6 3
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OD8 1.1 22.85 97030 5072 95 0.104 0.103 0.1208 0.124 0.138 RANDOM 8.29
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] -0.18 -0.12 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_3_deg 10.613 r_dihedral_angle_1_deg 6.328 r_scangle_it 3.269 r_scbond_it 2.643 r_mcangle_it 1.999 r_angle_refined_deg 1.73 r_mcbond_it 1.684 r_angle_other_deg 0.906
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.855 r_dihedral_angle_4_deg 15.07 r_dihedral_angle_3_deg 10.613 r_dihedral_angle_1_deg 6.328 r_scangle_it 3.269 r_scbond_it 2.643 r_mcangle_it 1.999 r_angle_refined_deg 1.73 r_mcbond_it 1.684 r_angle_other_deg 0.906 r_mcbond_other 0.631 r_symmetry_vdw_other 0.353 r_nbd_refined 0.233 r_nbd_other 0.213 r_xyhbond_nbd_refined 0.178 r_symmetry_hbond_refined 0.157 r_symmetry_vdw_refined 0.13 r_chiral_restr 0.12 r_nbtor_other 0.093 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 2333 Nucleic Acid Atoms Solvent Atoms 618 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling