8JQ4

Crystal structure of Lactobacillus rhamnosus L-rhamnose isomerase in complex with L-rhamnose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DE5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293PEG 550MME, MES
Crystal Properties
Matthews coefficientSolvent content
2.3547.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.116α = 90
b = 140.786β = 90
c = 147.345γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 2M2020-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0Photon FactoryAR-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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6146.931000.1150.120.0330.99916.713.3241662
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)RedundancyNumber Unique Reflections (All)
11.611.641001.4021.4580.3970.71113.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.6145.12272111188298.980.166750.164650.20789RANDOM19.681
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]
-0.12-0.180.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.801
r_dihedral_angle_4_deg18.52
r_dihedral_angle_3_deg14.507
r_dihedral_angle_1_deg6.822
r_rigid_bond_restr6.625
r_long_range_B_refined3.13
r_long_range_B_other2.806
r_scangle_other2.183
r_mcangle_other1.866
r_mcangle_it1.864
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.801
r_dihedral_angle_4_deg18.52
r_dihedral_angle_3_deg14.507
r_dihedral_angle_1_deg6.822
r_rigid_bond_restr6.625
r_long_range_B_refined3.13
r_long_range_B_other2.806
r_scangle_other2.183
r_mcangle_other1.866
r_mcangle_it1.864
r_scbond_it1.742
r_scbond_other1.741
r_mcbond_it1.447
r_mcbond_other1.439
r_angle_other_deg1.26
r_angle_refined_deg1.101
r_chiral_restr0.054
r_gen_planes_refined0.008
r_bond_refined_d0.003
r_bond_other_d0.003
r_gen_planes_other0.001
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 AtomsNumber
Protein Atoms13334
Nucleic Acid Atoms
Solvent Atoms1598
Heterogen Atoms85

Software

Software
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
MOLREPphasing