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Crystal Structure of Metal Free D-Xylose Isomerase.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1XIB 1XIB without metal ions and solvent
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 8 279 Crystallization from solution containing metal free enzyme at 20 mg/ml, 0.8M AmSO4, 2mM Pipes.
Crystallization occurred over 2 day period in sealed tubes., pH 8.0, SMALL TUBES, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.77 55.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.8 α = 90 b = 99.5 β = 90 c = 102.8 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 279 AREA DETECTOR SIEMENS-NICOLET X100 focussing nickel mirrors 1995-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 70.71 0.83 40569 2 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 86.6
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 1XIB without metal ions and solvent 1.8 70.71 40569 40237 2121 93.79 0.16124 0.15958 0.1473 0.19327 0.1813 RANDOM 17.994
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] -0.38 0.2 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_1_deg 5.304 r_scangle_it 5.192 r_scbond_it 3.281 r_mcangle_it 1.802 r_angle_refined_deg 1.739 r_mcbond_it 1.235 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.465 r_dihedral_angle_4_deg 16.095 r_dihedral_angle_3_deg 14.331 r_dihedral_angle_1_deg 5.304 r_scangle_it 5.192 r_scbond_it 3.281 r_mcangle_it 1.802 r_angle_refined_deg 1.739 r_mcbond_it 1.235 r_nbtor_refined 0.311 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.196 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.152 r_bond_refined_d 0.02 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3033 Nucleic Acid Atoms Solvent Atoms 374 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DATCOL data reduction XDS data scaling XTALVIEW refinement