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Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine at pH 5.8
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 5.8 20 MG/ML PROTEIN, 0.1 M MES 18% PEG 5KMME, 7.5% ISOPROPANOL, pH 5.80
Crystal Properties Matthews coefficient Solvent content 1.9 35.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.018 α = 90 b = 46.098 β = 90 c = 86.254 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 TORROIDAL MIRROR 2003-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 0.98 30 93.4 0.058 26.7 6.7 140638
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 0.98 2.02 89.1 0.406 4.23 5.3
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 0.98 26.82 133506 6992 93.2 0.119 0.118 0.1278 0.137 0.1445 RANDOM 7.04
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] -0.09 -0.21 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.919 r_dihedral_angle_1_deg 6.416 r_scangle_it 3.365 r_scbond_it 2.622 r_mcangle_it 2.106 r_mcbond_it 1.74 r_angle_refined_deg 1.727 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.35 r_nbd_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 11.919 r_dihedral_angle_1_deg 6.416 r_scangle_it 3.365 r_scbond_it 2.622 r_mcangle_it 2.106 r_mcbond_it 1.74 r_angle_refined_deg 1.727 r_angle_other_deg 0.881 r_symmetry_vdw_other 0.35 r_nbd_refined 0.327 r_nbd_other 0.242 r_xyhbond_nbd_refined 0.163 r_symmetry_hbond_refined 0.15 r_nbtor_other 0.133 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.121 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_gen_planes_other 0.001 r_bond_other_d r_dihedral_angle_2_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 2331 Nucleic Acid Atoms Solvent Atoms 641 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling