2PXC

Crystal structure of the Murray Valley Encephalitis Virus NS5 2'-O Methyltransferase domain in complex with SAM and GTPA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PX2PDB entry 2PX2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529312 % w/v PEG 20000, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.021α = 90
b = 81.021β = 90
c = 94.011γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-05-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97930ESRFID23-1

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
12.8301000.14123.212.88177-1.5
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)
12.82.91000.6952.613.1789

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 2PX22.830773241199.990.205470.202630.25634RANDOM42.987
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]
-0.68-0.681.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.017
r_dihedral_angle_3_deg16.074
r_dihedral_angle_4_deg15.222
r_scangle_it7.589
r_scbond_it5.454
r_dihedral_angle_1_deg4.407
r_mcangle_it4.269
r_mcbond_it3.29
r_angle_refined_deg1.253
r_mcbond_other0.815
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.017
r_dihedral_angle_3_deg16.074
r_dihedral_angle_4_deg15.222
r_scangle_it7.589
r_scbond_it5.454
r_dihedral_angle_1_deg4.407
r_mcangle_it4.269
r_mcbond_it3.29
r_angle_refined_deg1.253
r_mcbond_other0.815
r_angle_other_deg0.76
r_symmetry_hbond_refined0.258
r_symmetry_vdw_other0.232
r_nbd_refined0.2
r_nbd_other0.186
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.15
r_symmetry_vdw_refined0.114
r_nbtor_other0.084
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2086
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms127

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing