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Crystal structure of xylose isomerase from Piromyces E2 in complex with one Mg2+ ions and glycerol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5NH5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 294 13-16 % PEG 3350, 0.01 M MgCl2, 0,1 M Hepes pH 7
Crystal Properties Matthews coefficient Solvent content 2.3 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.606 α = 115.5 b = 79.365 β = 90.15 c = 92.096 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 2014-09-04 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 46.6 93.4 0.089 0.064 0.995 8.4 4 149911 6.5
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 80.7 0.35 0.26 0.688 2.6 3.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5NH5 1.8 46.46 142387 7495 93.35 0.19588 0.19412 0.22944 0.2323 RANDOM 18.034
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 -0.02 0.03 0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_4_deg 14.185 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 6.067 r_long_range_B_refined 4.584 r_long_range_B_other 4.584 r_scangle_other 1.754 r_angle_refined_deg 1.482 r_mcangle_other 1.135 r_mcangle_it 1.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.642 r_dihedral_angle_4_deg 14.185 r_dihedral_angle_3_deg 13.695 r_dihedral_angle_1_deg 6.067 r_long_range_B_refined 4.584 r_long_range_B_other 4.584 r_scangle_other 1.754 r_angle_refined_deg 1.482 r_mcangle_other 1.135 r_mcangle_it 1.134 r_scbond_it 1.128 r_scbond_other 1.128 r_angle_other_deg 1.123 r_mcbond_it 0.708 r_mcbond_other 0.707 r_chiral_restr 0.094 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 1638 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data scaling Aimless data scaling PHASER phasing XDS data reduction