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Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with D-allose
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 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.934 α = 90 b = 140.057 β = 90 c = 147.47 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 1.71 49.16 100 0.148 0.154 0.042 0.998 12.6 13.2 200687
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 1.71 1.74 99.7 1.338 1.393 0.386 0.7 12.7
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 1.71 46.43 190503 10079 99.95 0.14203 0.13967 0.1532 0.18702 0.1957 RANDOM 19.501
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] 0.23 -0.48 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.736 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.118 r_rigid_bond_restr 4.253 r_long_range_B_refined 2.681 r_long_range_B_other 2.612 r_scangle_other 2.206 r_mcangle_it 1.789 r_mcangle_other 1.789
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.736 r_dihedral_angle_4_deg 18.482 r_dihedral_angle_3_deg 13.87 r_dihedral_angle_1_deg 6.118 r_rigid_bond_restr 4.253 r_long_range_B_refined 2.681 r_long_range_B_other 2.612 r_scangle_other 2.206 r_mcangle_it 1.789 r_mcangle_other 1.789 r_scbond_it 1.706 r_scbond_other 1.706 r_mcbond_it 1.332 r_mcbond_other 1.329 r_angle_other_deg 1.325 r_angle_refined_deg 1.222 r_chiral_restr 0.06 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 13327 Nucleic Acid Atoms Solvent Atoms 986 Heterogen Atoms 104
Software Software Software Name Purpose Aimless data scaling XDS data reduction REFMAC refinement MOLREP phasing