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Crystal structure of native xylose isomerase from Piromyces E2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A0C 1A0C, 1A0D, 1A0E experimental model PDB 1A0D 1A0C, 1A0D, 1A0E experimental model PDB 1A0E 1A0C, 1A0D, 1A0E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 13-16 % PEG3350, HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.72 α = 115.33 b = 79.36 β = 90.31 c = 92.21 γ = 117
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 IMAGE PLATE MARRESEARCH 2014-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.79 41.2 92.3 0.045 0.034 0.998 20.6 3.9 150673 6.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.79 1.82 66.7 0.23 0.23 0.905 4.9 3.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 MOLECULAR REPLACEMENT THROUGHOUT 1A0C, 1A0D, 1A0E 1.8 41.2 143101 7550 93.01 0.12406 0.12281 0.137 0.14782 0.1576 RANDOM 14.927
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] -0.02 -0.02 0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.167 r_dihedral_angle_4_deg 14.914 r_dihedral_angle_3_deg 12.308 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 5.527 r_long_range_B_other 4.997 r_scangle_other 2.348 r_scbond_it 1.503 r_scbond_other 1.502 r_angle_refined_deg 1.488
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.167 r_dihedral_angle_4_deg 14.914 r_dihedral_angle_3_deg 12.308 r_dihedral_angle_1_deg 5.85 r_long_range_B_refined 5.527 r_long_range_B_other 4.997 r_scangle_other 2.348 r_scbond_it 1.503 r_scbond_other 1.502 r_angle_refined_deg 1.488 r_angle_other_deg 1.143 r_mcangle_it 1.087 r_mcangle_other 1.087 r_mcbond_it 0.673 r_mcbond_other 0.673 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.005 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13876 Nucleic Acid Atoms Solvent Atoms 2373 Heterogen Atoms 147
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing