2P3O

Crystal Structure of Dengue Methyltransferase in Complex with 7MeGpppA and S-Adenosyl-L-homocysteine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L9KPDB ENTRY 1L9K

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.82930.4 M Ammonium Sulfate, 0.1 M Sodium Citrate, 1.2 M Lithium Sulfate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.9458.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.56α = 90
b = 111.56β = 90
c = 56.33γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray1002000-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.993ESRFID14-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.75627.9697.10.08327.45.21032410025
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.7562.9597.10.5153.45.11448

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 1L9K2.75627.969592940960998.090.197830.194660.24372RANDOM65.565
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]
-2.2-1.1-2.23.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.239
r_dihedral_angle_4_deg22.944
r_dihedral_angle_3_deg18.451
r_dihedral_angle_1_deg6.426
r_scangle_it2.814
r_scbond_it1.67
r_angle_refined_deg1.615
r_mcangle_it1.161
r_mcbond_it0.685
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.239
r_dihedral_angle_4_deg22.944
r_dihedral_angle_3_deg18.451
r_dihedral_angle_1_deg6.426
r_scangle_it2.814
r_scbond_it1.67
r_angle_refined_deg1.615
r_mcangle_it1.161
r_mcbond_it0.685
r_nbtor_refined0.306
r_symmetry_vdw_refined0.281
r_nbd_refined0.228
r_symmetry_hbond_refined0.203
r_xyhbond_nbd_refined0.143
r_chiral_restr0.103
r_bond_refined_d0.013
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2022
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms135

Software

Software
Software NamePurpose
ADSCdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling