☰ Navigation Tabs
Xylanase Xyn10A from Streptomyces lividans in complex with xylobio-isofagomine lactam
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1E0X PDB ENTRY 1E0X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 20 MG/ML PROTEIN, 16% PEG 5K MME, 100 MM IMIDAZOLE, PH 7.5, 5% ISOPROPANOL
Crystal Properties Matthews coefficient Solvent content 1.9 35.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.814 α = 90 b = 45.878 β = 90 c = 85.737 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 2002-09-15 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 1.05 20 98 0.062 26.4 4.7 121638
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 1.05 1.09 86.4 0.441 2.3 2.05
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 1E0X 1.05 19.8 112969 5945 97.9 0.104 0.103 0.1188 0.126 0.1362 RANDOM 8.12
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] 0.11 0.04 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.229 r_scangle_it 4.558 r_scbond_it 3.441 r_mcangle_it 2.81 r_mcbond_it 2.03 r_angle_refined_deg 1.689 r_angle_other_deg 0.85 r_metal_ion_refined 0.614 r_nbd_other 0.455 r_symmetry_vdw_other 0.427
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.229 r_scangle_it 4.558 r_scbond_it 3.441 r_mcangle_it 2.81 r_mcbond_it 2.03 r_angle_refined_deg 1.689 r_angle_other_deg 0.85 r_metal_ion_refined 0.614 r_nbd_other 0.455 r_symmetry_vdw_other 0.427 r_symmetry_vdw_refined 0.382 r_metal_ion_other 0.335 r_nbd_refined 0.318 r_nbtor_other 0.298 r_chiral_restr 0.126 r_bond_refined_d 0.015 r_gen_planes_refined 0.004 r_bond_other_d r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbtor_refined r_xyhbond_nbd_refined r_xyhbond_nbd_other r_symmetry_hbond_refined 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 2324 Nucleic Acid Atoms Solvent Atoms 629 Heterogen Atoms 50
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling