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Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-fructose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ZFS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 magnesium chloride, Tris, PEG3350
Crystal Properties Matthews coefficient Solvent content 1.74 29.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.42 α = 90 b = 70.54 β = 90 c = 140.22 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2017-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 19.94 99.9 0.065 0.07 0.999 23.22 7.167 42687 25.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 100 0.522 0.017 1 3.64 7.3
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 5ZFS 1.8 19.94 40536 2087 99.9 0.127 0.126 0.1405 0.159 0.1718 RANDOM 19.37
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] -0.45 0.66 -0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 6.447 r_rigid_bond_restr 4.532 r_angle_other_deg 1.321 r_angle_refined_deg 1.217 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.616 r_dihedral_angle_4_deg 16.191 r_dihedral_angle_3_deg 14.063 r_dihedral_angle_1_deg 6.447 r_rigid_bond_restr 4.532 r_angle_other_deg 1.321 r_angle_refined_deg 1.217 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4462 Nucleic Acid Atoms Solvent Atoms 255 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PDB_EXTRACT data extraction MOLREP phasing