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Joint neutron and X-ray structure of apo-D-Xylose Isomerase at pH=5.9
NEUTRON DIFFRACTION - X-RAY DIFFRACTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GUB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5.9 280 crystals grew with ammonium sulfate as a precipitant at pH of 5.9, batch crystallization, temperature 280K
Crystal Properties Matthews coefficient Solvent content 2.78 55.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.908 α = 90 b = 99.503 β = 90 c = 102.971 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 position sensitive He3 2010-09-15 L TOF LAUE 2 1 x-ray 293 IMAGE PLATE RIGAKU RAXIS IV++ 2010-06-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 NUCLEAR REACTOR LANSCE BEAMLINE PCS 0.6-7.0 LANSCE PCS 2 ROTATING ANODE RIGAKU FR-E+ DW 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) 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 28.46 86.9 0.225 4.5 3 28290 28290 2.2 1.5 2 1.7 29.86 99.2 0.077 8.6 3.222 53087 53087
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 0.385 0.385 1.3 1.7 2 1.7 1.76 0.315 0.315 2.6 2.88
Refinement Statistics Diffraction ID Structure Solution Method Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 NEUTRON DIFFRACTION MOLECULAR REPLACEMENT 2 20 2.2 28290 26760 1347 81.4 0.254 0.254 0.28 RANDOM X-RAY DIFFRACTION MOLECULAR REPLACEMENT 1.7 20 2.5 49805 2507 93.6 0.254 0.195 0.1771 0.211 0.1887 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 x_dihedral_angle_d 17.9 x_dihedral_angle_d 17.9 x_angle_deg 1 x_angle_deg 1 x_improper_angle_d 0.82 x_improper_angle_d 0.82 x_bond_d 0.007 x_bond_d 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3054 Nucleic Acid Atoms Solvent Atoms 264 Heterogen Atoms
Software Software Software Name Purpose nCNS refinement d*TREK data scaling d*TREK data reduction LAUENORM data reduction LAUENORM data scaling