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Crystal structure of homo dimeric D-allulose 3-epimerase from Methylomonas sp. in complex with D-allulose
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 2 38.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.75 α = 90 b = 80.87 β = 90 c = 139.71 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 PIXEL DECTRIS PILATUS3 S 6M 2018-12-09 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 38.29 98.3 0.077 0.084 0.997 15.08 6.342 48196 27.311
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 97 0.464 0.506 0.918 3.92 6.315
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 38.29 45696 2439 98.27 0.1844 0.1806 0.1883 0.2545 0.2581 RANDOM 21.015
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 0.52 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.846 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.552 r_rigid_bond_restr 3.295 r_angle_other_deg 1.24 r_angle_refined_deg 1.173 r_chiral_restr 0.048 r_bond_other_d 0.004 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.846 r_dihedral_angle_4_deg 15.938 r_dihedral_angle_3_deg 15.188 r_dihedral_angle_1_deg 6.552 r_rigid_bond_restr 3.295 r_angle_other_deg 1.24 r_angle_refined_deg 1.173 r_chiral_restr 0.048 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_bond_refined_d 0.003 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4406 Nucleic Acid Atoms Solvent Atoms 468 Heterogen Atoms 26
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing