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Crystal structure of xylose isomerase from Piromyces sp. E2 in complex with two Mn2+ ions and sorbitol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NH5 D_1200004044
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 13-15 % PEG3350, 10 mM MnCl2, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.961 α = 115.67 b = 79.407 β = 89.44 c = 91.284 γ = 116.92
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 2015-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR-H 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.8 46.9 93.6 0.094 0.068 0.995 11.6 3.9 151276
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 1.8 1.83 79.6 0.482 0.378 0.583 2.1 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 D_1200004044 1.8 46.9 143710 7557 93.58 0.15674 0.15544 0.1624 0.18141 0.1858 RANDOM 15.707
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] -0.1 -0.03 0.06 0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.82 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_1_deg 5.743 r_long_range_B_refined 4.031 r_long_range_B_other 3.757 r_angle_refined_deg 1.477 r_scangle_other 1.279 r_angle_other_deg 0.954 r_mcangle_it 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.82 r_dihedral_angle_4_deg 13.151 r_dihedral_angle_3_deg 12.917 r_dihedral_angle_1_deg 5.743 r_long_range_B_refined 4.031 r_long_range_B_other 3.757 r_angle_refined_deg 1.477 r_scangle_other 1.279 r_angle_other_deg 0.954 r_mcangle_it 0.925 r_mcangle_other 0.925 r_scbond_it 0.81 r_scbond_other 0.783 r_mcbond_it 0.527 r_mcbond_other 0.526 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 1984 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing