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Crystal structure of L-ribulose 3-epimerase 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 293 20% PEG 4000, 0.1M Sodium citrate/Citric acid pH5.5, 10% 2-Propanol
Crystal Properties Matthews coefficient Solvent content 2.62 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 130.425 α = 90 b = 135.131 β = 90.06 c = 151.131 γ = 90
Symmetry Space Group P 1 21 1
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 EIGER X 16M 2019-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.5 47.2 98.34 0.096 0.114 0.06 0.996 8.25 3.5 625471
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.5 2.589 0.6174 0.7271 0.3809 0.853 1.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.5 30 169505 8921 98.22 0.20976 0.20737 0.25452 0.2318 RANDOM 47.309
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] -0.1 0.01 0.08 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.854 r_long_range_B_refined 9.171 r_long_range_B_other 9.17 r_dihedral_angle_1_deg 6.155 r_scangle_other 5.918 r_dihedral_angle_2_deg 5.215 r_mcangle_it 4.919 r_mcangle_other 4.919 r_scbond_it 3.62 r_scbond_other 3.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.854 r_long_range_B_refined 9.171 r_long_range_B_other 9.17 r_dihedral_angle_1_deg 6.155 r_scangle_other 5.918 r_dihedral_angle_2_deg 5.215 r_mcangle_it 4.919 r_mcangle_other 4.919 r_scbond_it 3.62 r_scbond_other 3.62 r_mcbond_it 3.132 r_mcbond_other 3.129 r_angle_refined_deg 1.262 r_angle_other_deg 0.436 r_chiral_restr 0.055 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg 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 35808 Nucleic Acid Atoms Solvent Atoms 582 Heterogen Atoms 415
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing