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Crystal structure of N-terminal His-tagged 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, HANGING DROP 7.5 293 Ethylene glycol, HEPES, PEG8000
Crystal Properties Matthews coefficient Solvent content 2.11 41.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.02 α = 99.3 b = 81.05 β = 101.5 c = 106.13 γ = 87.24
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 2.05 48.84 97.6 0.08 0.095 0.998 11.53 3.492 100753 30.924
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 2.05 2.1 96.9 0.496 0.584 0.835 2.78 3.57
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 2.05 48.84 95721 5031 97.68 0.1658 0.1618 0.1691 0.2414 0.2453 RANDOM 26.886
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 0.43 -0.23 0.61 0.38 -0.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.442 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 13.388 r_rigid_bond_restr 8.847 r_dihedral_angle_1_deg 6.374 r_angle_other_deg 1.191 r_angle_refined_deg 1.147 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.442 r_dihedral_angle_4_deg 16.557 r_dihedral_angle_3_deg 13.388 r_rigid_bond_restr 8.847 r_dihedral_angle_1_deg 6.374 r_angle_other_deg 1.191 r_angle_refined_deg 1.147 r_chiral_restr 0.042 r_bond_refined_d 0.003 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13288 Nucleic Acid Atoms Solvent Atoms 939 Heterogen Atoms 168
Software Software Software Name Purpose XDS data reduction XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing