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Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allulose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DE5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 PEG550MME, MES
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.887 α = 90 b = 139.445 β = 90 c = 146.834 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 2M 2020-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.73 48.94 100 0.118 0.123 0.033 0.999 17.5 13.4 192191
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 1.73 1.76 100 1.414 1.469 0.396 0.722 13.5
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.73 46.23 182641 9442 99.99 0.14174 0.13936 0.1509 0.18671 0.1934 RANDOM 21.6
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] 0.08 -0.32 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.131 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 6.27 r_rigid_bond_restr 4.796 r_long_range_B_refined 3.16 r_long_range_B_other 3.109 r_scangle_other 2.714 r_mcangle_other 2.303 r_mcangle_it 2.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.131 r_dihedral_angle_4_deg 18.686 r_dihedral_angle_3_deg 14.429 r_dihedral_angle_1_deg 6.27 r_rigid_bond_restr 4.796 r_long_range_B_refined 3.16 r_long_range_B_other 3.109 r_scangle_other 2.714 r_mcangle_other 2.303 r_mcangle_it 2.301 r_scbond_it 2.104 r_scbond_other 2.104 r_mcbond_it 1.737 r_mcbond_other 1.716 r_angle_other_deg 1.307 r_angle_refined_deg 1.262 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d r_gen_planes_other 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13531 Nucleic Acid Atoms Solvent Atoms 827 Heterogen Atoms 104
Software Software Software Name Purpose Aimless data scaling XDS data reduction REFMAC refinement MOLREP phasing