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Crystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions
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 294 13-15 % PEG3350, 0.1 M FeSO4, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.539 α = 115.57 b = 79.51 β = 89.96 c = 92.23 γ = 116.69
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 2014-10-07 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 2.4 45.3 85.8 0.148 0.127 0.963 5.9 3.5 59313 4.2
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 2.4 2.46 81.1 0.49 0.386 0.67 2.1 3.3
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 2.4 45.3 56358 2908 85.71 0.24648 0.24466 0.2543 0.28185 0.2892 RANDOM 28.773
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] -1.48 -0.56 0.66 0.13 0.46 0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.512 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_4_deg 14.693 r_dihedral_angle_1_deg 6.189 r_long_range_B_refined 2.535 r_long_range_B_other 2.476 r_angle_refined_deg 1.422 r_angle_other_deg 1.061 r_scbond_it 0.179 r_chiral_restr 0.078
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.512 r_dihedral_angle_3_deg 14.701 r_dihedral_angle_4_deg 14.693 r_dihedral_angle_1_deg 6.189 r_long_range_B_refined 2.535 r_long_range_B_other 2.476 r_angle_refined_deg 1.422 r_angle_other_deg 1.061 r_scbond_it 0.179 r_chiral_restr 0.078 r_mcangle_it 0.05 r_mcangle_other 0.05 r_mcbond_it 0.027 r_mcbond_other 0.026 r_scangle_other 0.025 r_bond_refined_d 0.012 r_scbond_other 0.011 r_gen_planes_refined 0.006 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 13866 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 23
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing