3QDF

Crystal structure of 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Mycobacterium marinum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DFU2dfu molecule A, protein only

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5289MymaA.00471.a.A1 PW30262 at 26.1 mg/mL against PACT screen condition A12, 10 mM ZnCl2, 0.1 M NaOAc pH 5.0, 20% PEG 6000 and cryo-protected with 25% ethylene glycol, crystal tracking ID 218461a12, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
3.0559.67

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.7α = 90
b = 104.93β = 90
c = 136.97γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2011-01-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.055098.50.07614.424.22207021732-331.963
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.191.90.4612.92.81597

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUT2dfu molecule A, protein only2.055021644111998.070.1850.18260.2294RANDOM26.6039
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]
-0.021.14-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg18.091
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg6.641
r_scangle_it2.717
r_scbond_it1.668
r_angle_refined_deg1.377
r_mcangle_it1.073
r_mcbond_it0.62
r_chiral_restr0.087
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.929
r_dihedral_angle_4_deg18.091
r_dihedral_angle_3_deg13.046
r_dihedral_angle_1_deg6.641
r_scangle_it2.717
r_scbond_it1.668
r_angle_refined_deg1.377
r_mcangle_it1.073
r_mcbond_it0.62
r_chiral_restr0.087
r_bond_refined_d0.013
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1862
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms14

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction