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Crystal structure of xylose isomerase from Piromyces E2 in complex with two Ca2+ 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 294 13-15 % PEG3350, 10 mM CaCl2, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.764 α = 115.41 b = 79.337 β = 89.91 c = 91.926 γ = 117.16
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 2015-02-25 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 1.86 46.7 92.6 0.09 0.071 0.995 10.6 4 136386 9.3
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 1.86 1.89 75.7 0.488 0.384 0.602 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 1.86 46.7 129514 6829 93.67 0.17712 0.17585 0.1824 0.20136 0.207 RANDOM 20.21
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] -0.19 -0.11 0.07 0.03 0.07 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_4_deg 12.574 r_dihedral_angle_1_deg 5.684 r_long_range_B_refined 4.9 r_long_range_B_other 4.554 r_scangle_other 1.522 r_angle_refined_deg 1.238 r_mcangle_it 1.162 r_mcangle_other 1.162
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.041 r_dihedral_angle_3_deg 13.042 r_dihedral_angle_4_deg 12.574 r_dihedral_angle_1_deg 5.684 r_long_range_B_refined 4.9 r_long_range_B_other 4.554 r_scangle_other 1.522 r_angle_refined_deg 1.238 r_mcangle_it 1.162 r_mcangle_other 1.162 r_scbond_it 0.984 r_scbond_other 0.948 r_angle_other_deg 0.929 r_mcbond_it 0.69 r_mcbond_other 0.69 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.003 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 1620 Heterogen Atoms 160
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing