3FHY

Crystal structure of D235N mutant of human pyridoxal kinase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YXUPDB entry 2YXU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8298Protein solution: 20 mM Sodium BES buffer pH 7.2, 100 mM NaCl, 5 mM BME, 2.5 mM MgATP. Precipitant: 100 mM Tris-HCl pH 8.0, 57%, MPD, 5 mM MgSO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1560.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.11α = 90
b = 114.643β = 90
c = 169.681γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVMSC Varimax confocal optics2008-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

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
12.332.54990.0493.3939415
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)
2.32.3899.30.254.63.183924

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2YXU2.329.363941039410195498.80.2190.2190.2140.261RANDOM45.209
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]
16.26-8.17-8.09
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22.9
c_scangle_it10.71
c_scbond_it9.4
c_mcangle_it7.77
c_mcbond_it6.19
c_angle_deg1.4
c_improper_angle_d0.95
c_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4828
Nucleic Acid Atoms
Solvent Atoms264
Heterogen Atoms126

Software

Software
Software NamePurpose
d*TREKdata processing
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing