2RDX

Crystal structure of mandelate racemase/muconate lactonizing enzyme from Roseovarius nubinhibens ISM


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52940.1M HEPES pH 7.5, 30% PEG MME550, 10% Glycerol, 50mM Magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.4148.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.415α = 90
b = 169.219β = 90
c = 223.476γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2007-06-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9796APS31-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
125096.70.1080.0783.62.7215416-0.528.8
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)
122.07960.660.760.62.4

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 DIFFRACTIONSADTHROUGHOUT220204242635197.90.1960.1940.256RANDOM28.48
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]
-1.310.061.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.688
r_dihedral_angle_3_deg17.148
r_dihedral_angle_4_deg15.461
r_scangle_it14.136
r_scbond_it11.718
r_mcangle_it7.532
r_mcbond_it6.245
r_dihedral_angle_1_deg5.593
r_angle_refined_deg1.264
r_nbtor_refined0.295
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.688
r_dihedral_angle_3_deg17.148
r_dihedral_angle_4_deg15.461
r_scangle_it14.136
r_scbond_it11.718
r_mcangle_it7.532
r_mcbond_it6.245
r_dihedral_angle_1_deg5.593
r_angle_refined_deg1.264
r_nbtor_refined0.295
r_xyhbond_nbd_refined0.163
r_nbd_refined0.147
r_symmetry_hbond_refined0.124
r_metal_ion_refined0.119
r_symmetry_vdw_refined0.111
r_chiral_restr0.079
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms22587
Nucleic Acid Atoms
Solvent Atoms1025
Heterogen Atoms50

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing