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Time-of-Flight Neutron Diffraction Structure of D-Xylose Isomerase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 LIQUID DIFFUSION 8 293 50mM tris-HCl,38%AMSO4,2mM Mn2+ and 2mM Co2+,XI @ 125mg/ml, pH 8.0, LIQUID DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.88 α = 90 b = 99.68 β = 90 c = 102.9 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 neutron 293 AREA DETECTOR Time-of-Flight Multiwire He3 neutron detector 2003-09-15 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 0.7-7.0
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 1.8 20 78 0.185 34394 34394 3 1.5
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 1.8 1.94 39 0.262 3692
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 1XIB 2.2 10 3 23312 23312 1184 0.271 0.268 0.319 5%, 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]
RMS Deviations Key Refinement Restraint Deviation s_angle_d 0.173 s_anti_bump_dis_restr 0.168 s_non_zero_chiral_vol 0.055 s_zero_chiral_vol 0.036 s_bond_d 0.032
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 512 Heterogen Atoms 2
Software Software Software Name Purpose d*TREK data reduction SHELXL-97 model building SHELXL-97 refinement d*TREK data scaling SHELXL-97 phasing