2AUT

Crystal structure of Lys154Asn mutant of mature AphA of S. typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Z5GPartially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A random error of 0.2A was added to the atomic coordinates of the starting model.

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1vapour diffusion sitting-drop, micro-seeding4.7293PEG 6000, magnesium chloride, sodium acetate, dihydrogen phosphate , pH 4.7, vapour diffusion sitting-drop, micro-seeding, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3447.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.737α = 90
b = 84.477β = 90
c = 149.268γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMARRESEARCHOSMIC mirror2004-01-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.243094.50.05513.53.4408094067124.77
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)
2.242.3691.40.1627.13.25241

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPartially refined structure of wild-type APHA (PDB code 1Z5G) with all HET atoms (HOH, MG etc.) removed and side chain of Lys154 replaced with ALA was used as the starting model. A random error of 0.2A was added to the atomic coordinates of the starting model.2.252040554405542004940.1510.197random24.29
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]
0.142-4.8024.659
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.09
c_scangle_it3.2
c_mcangle_it2.22
c_scbond_it2.17
c_mcbond_it1.4
c_angle_deg1
c_improper_angle_d0.833
c_bond_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6589
Nucleic Acid Atoms
Solvent Atoms534
Heterogen Atoms10

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
TRUNCATEdata scaling
CNSphasing