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Crystal structure of N-terminal His-tagged D-allulose 3-epimerase from Methylomonas sp. with additional C-terminal residues
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 7.5 293 Ethylene glycol, HEPES, PEG8000
Crystal Properties Matthews coefficient Solvent content 2.26 45.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.43 α = 87.67 b = 92.77 β = 98.64 c = 93.78 γ = 115.6
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 2019-05-17 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 1.58 45.71 94 0.034 0.041 0.999 22.43 3.472 311350 25.715
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 1.58 1.62 94.7 0.457 0.538 0.83 2.82 3.63
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 1.58 45.71 295623 15718 94.02 0.1792 0.1767 0.1876 0.2269 0.235 RANDOM 20.931
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] -0.33 0.02 -0.36 0.15 0.21 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.489 r_dihedral_angle_4_deg 15.848 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 6.347 r_rigid_bond_restr 4.695 r_angle_other_deg 1.336 r_angle_refined_deg 1.252 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.489 r_dihedral_angle_4_deg 15.848 r_dihedral_angle_3_deg 13.976 r_dihedral_angle_1_deg 6.347 r_rigid_bond_restr 4.695 r_angle_other_deg 1.336 r_angle_refined_deg 1.252 r_chiral_restr 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17677 Nucleic Acid Atoms Solvent Atoms 2158 Heterogen Atoms 252
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing