5IKM | pdb_00005ikm

1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex with S-Adenosylmethionine and Beta-D-Fructopyranose.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4V0Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5292Protein: 6.8 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3); Screen: JCSG+ (E2), 0.2M Sodium chloride, 0.1M Sodium cacodylate (pH 6.5) 2M Ammonium sulfate; Cryo: 4M Ammonium sulfate : 50% Sucrose (1:1).
Crystal Properties
Matthews coefficientSolvent content
2.9958.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.38α = 90
b = 86.23β = 90
c = 144.307γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2014-12-11MSINGLE 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)R Sym I (Observed)CC (Half)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
11.93099.30.1110.1110.88216.25.929015-317
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)
11.91.931000.6413.95.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4V0Q1.929.1927572138699.30.154490.152990.16340.184220.1896RANDOM19.827
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]
-1.13-1.933.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.199
r_dihedral_angle_4_deg10.945
r_dihedral_angle_3_deg10.51
r_long_range_B_refined7.079
r_long_range_B_other6.683
r_dihedral_angle_1_deg3.356
r_scangle_other2.052
r_angle_refined_deg1.505
r_scbond_it1.278
r_scbond_other1.275
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.199
r_dihedral_angle_4_deg10.945
r_dihedral_angle_3_deg10.51
r_long_range_B_refined7.079
r_long_range_B_other6.683
r_dihedral_angle_1_deg3.356
r_scangle_other2.052
r_angle_refined_deg1.505
r_scbond_it1.278
r_scbond_other1.275
r_mcangle_it1.108
r_mcangle_other1.107
r_angle_other_deg0.866
r_mcbond_it0.64
r_mcbond_other0.639
r_chiral_restr0.09
r_gen_planes_refined0.023
r_gen_planes_other0.018
r_bond_refined_d0.01
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2053
Nucleic Acid Atoms
Solvent Atoms282
Heterogen Atoms100

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing