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Crystal structure of xylose isomerase from Piromyces E2 in complex with 2 Ni2+ ions and xylose
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 NiCl2, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.719 α = 115.14 b = 79.04 β = 90.36 c = 92.01 γ = 117.01
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 2014-10-09 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 39.4 91.4 0.088 0.067 0.993 8 3.8 146916 5.7
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 87.3 0.491 0.361 0.719 1.9 3.8
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 39.4 139501 7382 91.4 0.15455 0.15349 0.1633 0.17478 0.184 RANDOM 19.449
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] -0.16 -0.02 0.01 0.05 0.01 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 12.875 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 5.784 r_long_range_B_refined 5.399 r_long_range_B_other 5.109 r_scangle_other 2.287 r_scbond_it 1.486 r_scbond_other 1.451 r_angle_refined_deg 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.912 r_dihedral_angle_4_deg 12.875 r_dihedral_angle_3_deg 12.786 r_dihedral_angle_1_deg 5.784 r_long_range_B_refined 5.399 r_long_range_B_other 5.109 r_scangle_other 2.287 r_scbond_it 1.486 r_scbond_other 1.451 r_angle_refined_deg 1.37 r_mcangle_other 1.306 r_mcangle_it 1.305 r_angle_other_deg 1.017 r_mcbond_it 0.813 r_mcbond_other 0.81 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.005 r_gen_planes_other 0.004 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 13871 Nucleic Acid Atoms Solvent Atoms 1751 Heterogen Atoms 223
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing