3LL4

Structure of the H13A mutant of Ykr043C in complex with fructose-1,6-bisphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3F3KPDB entry 3F3K molecule A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5294resevoir of 0.1M Sodium Hepes ph7.5, 10% isopropanol and 20% PEG4K. 0.03 mg/ml trypsin was added to the protein prior to crystallization setup. Crystals were washed in well solution, then soaked in well solution plus 12% Glycerol and 0.1M fructose 1,6 bis-phosphate at room temperature for 10 minutes prior to flash-freezing in liquid N2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.6753.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.62α = 90
b = 84.022β = 90
c = 101.568γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++mirrors2009-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
12.531.39980.1040.10421.2852568325181-340.9
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)
12.52.5489.10.4844.74.91215

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 REPLACEMENTTHROUGHOUTPDB entry 3F3K molecule A2.4931.392516023890127097.630.224680.222540.2663RANDOM28.3
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]
-0.010.03-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.353
r_dihedral_angle_3_deg16.567
r_dihedral_angle_4_deg15.494
r_dihedral_angle_1_deg6.175
r_scangle_it2.884
r_scbond_it1.837
r_angle_refined_deg1.554
r_mcangle_it1.137
r_mcbond_it0.651
r_nbtor_refined0.31
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4208
Nucleic Acid Atoms
Solvent Atoms57
Heterogen Atoms40

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling