4GMK

Crystal Structure of Ribose 5-Phosphate Isomerase from the Probiotic Bacterium Lactobacillus salivarius UCC118


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.52930.8M NaH2PO4/1.2M K2HPO4, 0.1M acetate, pH4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.34α = 90
b = 63.8β = 107.68
c = 59.84γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 2M2011-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.917DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.7234.5499.24932148927
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.7699.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7234.544932146452247099.070.171490.16970.20596RANDOM23.779
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]
0.02-0.030.03-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.873
r_dihedral_angle_4_deg15.837
r_dihedral_angle_3_deg14.796
r_dihedral_angle_1_deg5.798
r_angle_refined_deg1.929
r_chiral_restr0.132
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg44.873
r_dihedral_angle_4_deg15.837
r_dihedral_angle_3_deg14.796
r_dihedral_angle_1_deg5.798
r_angle_refined_deg1.929
r_chiral_restr0.132
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3470
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms17

Software

Software
Software NamePurpose
GDAdata collection
REFMACrefinement
xia2data reduction
xia2data scaling