8KDZ | pdb_00008kdz

DENGUE 3 NS5 METHYLTRANSFERASE BOUND TO S-Adenosyl-L-homocysteine and Caffeic acid phenethyl ester


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4R8R 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529325% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.412238649.041695

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.648α = 90
b = 60.722β = 90
c = 184.36γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2023-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)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
12.623.05698.60.1887.36108535
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.7299.30.421

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4R8R2.623.05610853592499.3280.2330.2310.23230.27270.273928.803
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]
-2.711-2.1224.833
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.516
r_dihedral_angle_4_deg18.661
r_dihedral_angle_3_deg18.259
r_lrange_it7.097
r_dihedral_angle_1_deg5.843
r_scangle_it3.32
r_mcangle_it2.489
r_scbond_it2.136
r_angle_refined_deg1.558
r_mcbond_it1.501
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.516
r_dihedral_angle_4_deg18.661
r_dihedral_angle_3_deg18.259
r_lrange_it7.097
r_dihedral_angle_1_deg5.843
r_scangle_it3.32
r_mcangle_it2.489
r_scbond_it2.136
r_angle_refined_deg1.558
r_mcbond_it1.501
r_ext_dist_refined_d0.337
r_nbtor_refined0.312
r_symmetry_nbd_refined0.28
r_symmetry_xyhbond_nbd_refined0.265
r_nbd_refined0.214
r_xyhbond_nbd_refined0.149
r_ncsr_local_group_10.117
r_chiral_restr0.097
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4086
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms94

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing