4IV8

Crystal structure of N-methyl transferase from Plasmodium knowlesi complexed with S-adenosyl methionine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UJ7 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5282Protein solution was at 15 mg/mL containing 20 mM Tris, 100 mM NaCl, 2 mM EDTA and 5 mM bME, 5 mM SAM. Mother liqueur contained 0.1 M Na-acetate (pH 5.0) and 20% PEG 3.350. Cryoprotectant was 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 282K
Crystal Properties
Matthews coefficientSolvent content
2.3848.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.71α = 90
b = 96.76β = 90
c = 38.46γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002012-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.92099.80.08912.815110251018-330.857
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)
11.91.951000.7482.56

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 REPLACEMENTTHROUGHOUT3UJ71.919.75101650979254999.830.2530.23470.23280.2708RANDOM27.0975
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]
-0.090.030.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.762
r_dihedral_angle_3_deg13.938
r_dihedral_angle_4_deg10.74
r_dihedral_angle_1_deg5.082
r_angle_refined_deg1.147
r_chiral_restr0.079
r_bond_refined_d0.007
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4048
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms62

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing