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Xylose Isomerase in Substrate and Inhibitor Michaelis States: Atomic Resolution Studies of a Metal-Mediated Hydride Shift
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XYA STREPTOMYCES OLIVOCHROMOGENES XYLOSE ISOMERASE - PDB ID 1XYA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 2.1M (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 398K
Crystal Properties Matthews coefficient Solvent content 2.15 42.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.865 α = 90 b = 92.968 β = 90 c = 98.298 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 ADSC MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 1.0 APS 14-BM-C
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 50 93.6 0.053 24.1 4.6 229134 212189
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 1.02 83.4 0.473 2.3 2.9
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-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 STREPTOMYCES OLIVOCHROMOGENES XYLOSE ISOMERASE - PDB ID 1XYA 0.98 50 212189 212189 10601 94.9 0.1111 0.1109 0.1453 0.1293 0.1467 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 58 2924.75 3448.32
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.105 s_zero_chiral_vol 0.101 s_non_zero_chiral_vol 0.101 s_anti_bump_dis_restr 0.095 s_similar_adp_cmpnt 0.048 s_angle_d 0.032 s_from_restr_planes 0.026 s_bond_d 0.017 s_rigid_bond_adp_cmpnt 0.006 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3025 Nucleic Acid Atoms Solvent Atoms 411 Heterogen Atoms 16
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement HKL-2000 data collection HKL-2000 data reduction CNS phasing