2PX2

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAH (Monoclinic form 1)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.5mM SAH, 0.2M Calcium chloride, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1241.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.4α = 90
b = 68.3β = 98.4
c = 82γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-11-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97626ESRFBM14

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
123092.60.07115.53.131650-1.5
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)
22.07600.2452.61.72026

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 1L9K227.426662141581.660.20390.200120.27314RANDOM34.372
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]
-1.221.02-2.574.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.044
r_dihedral_angle_3_deg15.391
r_dihedral_angle_4_deg14.905
r_scangle_it10.153
r_scbond_it7.933
r_mcangle_it5.821
r_mcbond_it5.67
r_dihedral_angle_1_deg5.236
r_mcbond_other1.677
r_angle_refined_deg1.374
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.044
r_dihedral_angle_3_deg15.391
r_dihedral_angle_4_deg14.905
r_scangle_it10.153
r_scbond_it7.933
r_mcangle_it5.821
r_mcbond_it5.67
r_dihedral_angle_1_deg5.236
r_mcbond_other1.677
r_angle_refined_deg1.374
r_angle_other_deg0.851
r_symmetry_vdw_other0.254
r_symmetry_hbond_refined0.227
r_xyhbond_nbd_refined0.207
r_nbd_refined0.202
r_nbd_other0.2
r_symmetry_vdw_refined0.189
r_nbtor_refined0.179
r_nbtor_other0.085
r_chiral_restr0.076
r_bond_refined_d0.012
r_bond_other_d0.006
r_gen_planes_refined0.004
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4017
Nucleic Acid Atoms
Solvent Atoms333
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing