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Crystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ 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, 0.1 mM CdCl2, 0.1 M Hepes pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.64 α = 115.37 b = 79.37 β = 89.97 c = 92.01 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 2014-10-27 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 45.1 87.8 0.063 0.059 0.995 9.4 2 128136 9.4
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 55.9 0.386 0.361 0.644 2 1.8
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 1.86 45.1 121647 6456 88.25 0.14163 0.1404 0.1506 0.16474 0.174 RANDOM 17.651
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] -0.09 -0.05 0.06 0.01 0.04 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_4_deg 14.569 r_dihedral_angle_3_deg 13.683 r_dihedral_angle_1_deg 5.781 r_long_range_B_refined 5.354 r_long_range_B_other 4.977 r_scangle_other 2.182 r_scbond_it 1.462 r_angle_refined_deg 1.422 r_scbond_other 1.385
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.55 r_dihedral_angle_4_deg 14.569 r_dihedral_angle_3_deg 13.683 r_dihedral_angle_1_deg 5.781 r_long_range_B_refined 5.354 r_long_range_B_other 4.977 r_scangle_other 2.182 r_scbond_it 1.462 r_angle_refined_deg 1.422 r_scbond_other 1.385 r_mcangle_it 1.187 r_mcangle_other 1.187 r_angle_other_deg 1.023 r_mcbond_it 0.717 r_mcbond_other 0.716 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 13876 Nucleic Acid Atoms Solvent Atoms 1837 Heterogen Atoms 208
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling PHASER phasing