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Crystal structure of beta-1,3-xylanase from Vibrio sp. AX-4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 9.5 293 1M sodium citrate, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K 2 VAPOR DIFFUSION, HANGING DROP 9.5 293 1M sodium citrate, 0.1M CHES, 20% glycerol, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.873 α = 90 b = 75.654 β = 90 c = 82.119 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 QUANTUM 210 2003-12-21 M MAD 2 1 x-ray 100 CCD ADSC QUANTUM 315 2004-04-27 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 0.974, 0.978, 0.960 Photon Factory AR-NW12A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.900 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 0.86 50 96.9 0.075 11.4 7 272709 264110 5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1,2 0.86 0.89 74.7 0.503 2.9 20202
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 0.86 19.85 250801 13309 96.85 0.13988 0.13946 0.149 0.14772 0.1563 RANDOM 6.847
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] -0.01 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_3_deg 10.976 r_dihedral_angle_1_deg 5.746 r_sphericity_free 2.226 r_sphericity_bonded 1.857 r_scangle_it 1.683 r_scbond_it 1.281 r_angle_refined_deg 1.185 r_mcangle_it 0.928
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.891 r_dihedral_angle_4_deg 13.85 r_dihedral_angle_3_deg 10.976 r_dihedral_angle_1_deg 5.746 r_sphericity_free 2.226 r_sphericity_bonded 1.857 r_scangle_it 1.683 r_scbond_it 1.281 r_angle_refined_deg 1.185 r_mcangle_it 0.928 r_rigid_bond_restr 0.9 r_angle_other_deg 0.816 r_mcbond_it 0.727 r_symmetry_vdw_refined 0.586 r_mcbond_other 0.286 r_nbd_refined 0.201 r_symmetry_vdw_other 0.194 r_nbtor_refined 0.183 r_nbd_other 0.178 r_symmetry_hbond_refined 0.115 r_xyhbond_nbd_refined 0.091 r_nbtor_other 0.087 r_chiral_restr 0.073 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.003 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2540 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling SOLVE phasing