3PM6

Crystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ISV 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP528923.4 mg/mL CoimA.00345.a.A1 PS00465 against ProPlex screen condition E11, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, soaked into 1 M NaI, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, 20% ethylene glycol, crystal tracking ID 206915e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2845.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.91α = 90
b = 77.77β = 93.71
c = 68.32γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944Osmic VariMax HF2010-10-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.25097.50.10412.967.33082630048-334.628
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)
12.22.2682.80.4783.762254

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 DIFFRACTIONSAD WITH MRTHROUGHOUT2isv2.25030008150597.350.19980.19780.2369RANDOM27.6569
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]
-0.51.32-0.761.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_4_deg22.928
r_dihedral_angle_3_deg14.998
r_dihedral_angle_1_deg5.506
r_scangle_it3.425
r_scbond_it2.11
r_angle_refined_deg1.428
r_mcangle_it1.298
r_mcbond_it0.708
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.496
r_dihedral_angle_4_deg22.928
r_dihedral_angle_3_deg14.998
r_dihedral_angle_1_deg5.506
r_scangle_it3.425
r_scbond_it2.11
r_angle_refined_deg1.428
r_mcangle_it1.298
r_mcbond_it0.708
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4114
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms35

Software

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