8ZMC | pdb_00008zmc

Dengue 3 NS5 methyltransferase bound to S-Adenosyl-L-homocysteine and Herbacetin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293.1525% PEG 8000 100 mM Tris 200 mM NaCl 20 mM Trisodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.3547.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.877α = 90
b = 59.966β = 90
c = 185.044γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPix-6000HE2024-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54184

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.824.89299.90.20.99213.819.620387
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.950.8974.6

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-VALUE4R8R2.824.8921458670799.6790.2610.25890.25930.30250.295136.984
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]
-4.265-4.4018.666
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.006
r_dihedral_angle_2_deg16.285
r_dihedral_angle_6_deg15.934
r_lrange_it6.869
r_dihedral_angle_1_deg5.429
r_scangle_it3.454
r_mcangle_it2.454
r_scbond_it2.182
r_angle_refined_deg2.124
r_mcbond_it1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.006
r_dihedral_angle_2_deg16.285
r_dihedral_angle_6_deg15.934
r_lrange_it6.869
r_dihedral_angle_1_deg5.429
r_scangle_it3.454
r_mcangle_it2.454
r_scbond_it2.182
r_angle_refined_deg2.124
r_mcbond_it1.45
r_symmetry_xyhbond_nbd_refined0.592
r_symmetry_nbd_refined0.33
r_nbtor_refined0.309
r_nbd_refined0.221
r_xyhbond_nbd_refined0.154
r_chiral_restr0.098
r_ext_dist_refined_b0.047
r_bond_refined_d0.007
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4078
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling
MOLREPphasing