☰ Navigation Tabs
Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with L-rhamnose
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 PEG 550MME, MES
Crystal Properties Matthews coefficient Solvent content 2.35 47.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.116 α = 90 b = 140.786 β = 90 c = 147.345 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 1.61 46.93 100 0.115 0.12 0.033 0.999 16.7 13.3 241662
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 1.61 1.64 100 1.402 1.458 0.397 0.711 13.4
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 1.61 45.1 227211 11882 98.98 0.16675 0.16465 0.1772 0.20789 0.2183 RANDOM 19.681
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] -0.12 -0.18 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.801 r_dihedral_angle_4_deg 18.52 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 6.822 r_rigid_bond_restr 6.625 r_long_range_B_refined 3.13 r_long_range_B_other 2.806 r_scangle_other 2.183 r_mcangle_other 1.866 r_mcangle_it 1.864
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.801 r_dihedral_angle_4_deg 18.52 r_dihedral_angle_3_deg 14.507 r_dihedral_angle_1_deg 6.822 r_rigid_bond_restr 6.625 r_long_range_B_refined 3.13 r_long_range_B_other 2.806 r_scangle_other 2.183 r_mcangle_other 1.866 r_mcangle_it 1.864 r_scbond_it 1.742 r_scbond_other 1.741 r_mcbond_it 1.447 r_mcbond_other 1.439 r_angle_other_deg 1.26 r_angle_refined_deg 1.101 r_chiral_restr 0.054 r_gen_planes_refined 0.008 r_bond_refined_d 0.003 r_bond_other_d 0.003 r_gen_planes_other 0.001 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 13334 Nucleic Acid Atoms Solvent Atoms 1598 Heterogen Atoms 85
Software Software Software Name Purpose Aimless data scaling XDS data reduction REFMAC refinement MOLREP phasing