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Crystal structure of reducing-end-xylose releasing exo-oligoxylanase Y198F mutant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WU4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 PEG4000, SODIUM ACETATE, GLYCEROL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.18 43.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.191 α = 90 b = 86.207 β = 90 c = 87.729 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 95 CCD ADSC QUANTUM 4 2007-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.00000 Photon Factory BL-17A
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 1.39 50 99.7 0.079 32.1 3.7 81959 81761 19.7
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 1.39 1.44 97.6 0.384 3.5 3.4
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 1WU4 1.39 45.5 81677 4098 99.91 0.178 0.177 0.1746 0.198 0.1942 RANDOM 14.73
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 12.055 r_dihedral_angle_3_deg 11.829 r_dihedral_angle_1_deg 5.439 r_scangle_it 2.528 r_scbond_it 1.641 r_angle_refined_deg 1.163 r_mcangle_it 1.102 r_mcbond_it 0.596 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.134 r_dihedral_angle_4_deg 12.055 r_dihedral_angle_3_deg 11.829 r_dihedral_angle_1_deg 5.439 r_scangle_it 2.528 r_scbond_it 1.641 r_angle_refined_deg 1.163 r_mcangle_it 1.102 r_mcbond_it 0.596 r_chiral_restr 0.087 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3084 Nucleic Acid Atoms Solvent Atoms 516 Heterogen Atoms 25
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling HKL-2000 data scaling