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The 0.86 Angstrom Structure of Xylose Isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XYA PDB ENTRY 1XYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 10mM MgCl2, 2.2M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.97 37.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.906 α = 90 b = 92.883 β = 90 c = 98.321 γ = 90
Symmetry Space Group I 2 2 2
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 SBC-2 MIRROR 2002-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.918 APS 19-ID
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 0.8 50 97.4 0.051 17.8 4.8 358727 358727 1 1
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 0.8 0.9 92 0.565 1.8 2.4 37312
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R PDB ENTRY 1XYA 0.86 50 358727 358727 17954 100 0.1255 0.1255 0.1244 0.1031 0.1431 0.1086 RANDOM
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 88 2913.39 3477.06
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.116 s_zero_chiral_vol 0.102 s_non_zero_chiral_vol 0.095 s_similar_adp_cmpnt 0.046 s_angle_d 0.033 s_from_restr_planes 0.0271 s_bond_d 0.016 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist s_anti_bump_dis_restr
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 449 Heterogen Atoms 5
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement HKL-2000 data collection HKL-2000 data reduction CNS phasing