3IST

Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7293PEG3350 15%, Succinic acid 0.1M, pH 7, 10mm L-Glutamic acid, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3948.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.42α = 90
b = 66.42β = 90
c = 258.774γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rmirrors2009-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97934APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (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
11.655097.90.0730.07339.46.56972469724-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6892.60.6710.6712.44.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT3hfr1.65506607866078351298.010.173070.17110.21145RANDOM11.555
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]
0.980.98-1.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.906
r_dihedral_angle_4_deg14.149
r_dihedral_angle_3_deg12.635
r_dihedral_angle_1_deg5.664
r_scangle_it4.759
r_scbond_it3.11
r_mcangle_it1.687
r_angle_refined_deg1.677
r_angle_other_deg0.998
r_mcbond_it0.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.906
r_dihedral_angle_4_deg14.149
r_dihedral_angle_3_deg12.635
r_dihedral_angle_1_deg5.664
r_scangle_it4.759
r_scbond_it3.11
r_mcangle_it1.687
r_angle_refined_deg1.677
r_angle_other_deg0.998
r_mcbond_it0.971
r_mcbond_other0.31
r_chiral_restr0.108
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.006
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4071
Nucleic Acid Atoms
Solvent Atoms483
Heterogen Atoms18

Software

Software
Software NamePurpose
HKL-2000data collection
HKL-3000phasing
REFMACrefinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling