2PX4

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52931.6 M Magnesium sulfate, 0.1 M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.3647.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.4α = 90
b = 68.2β = 115.6
c = 50.2γ = 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 BM140.97650ESRFBM14

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
12.23096.50.09113.85.213890-1.5
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)
12.22.377.20.2732.83.41109

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 2PX22.226.441322667696.390.164630.161380.22927RANDOM32.592
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]
1.721.95-0.90.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.77
r_dihedral_angle_4_deg15.01
r_dihedral_angle_3_deg12.273
r_scangle_it7.276
r_scbond_it5.505
r_dihedral_angle_1_deg4.7
r_mcangle_it3.701
r_mcbond_it3.501
r_angle_refined_deg1.037
r_mcbond_other0.896
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.77
r_dihedral_angle_4_deg15.01
r_dihedral_angle_3_deg12.273
r_scangle_it7.276
r_scbond_it5.505
r_dihedral_angle_1_deg4.7
r_mcangle_it3.701
r_mcbond_it3.501
r_angle_refined_deg1.037
r_mcbond_other0.896
r_angle_other_deg0.78
r_symmetry_vdw_other0.234
r_nbd_refined0.183
r_nbd_other0.182
r_symmetry_vdw_refined0.177
r_nbtor_refined0.172
r_symmetry_hbond_refined0.172
r_xyhbond_nbd_refined0.151
r_nbtor_other0.081
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2074
Nucleic Acid Atoms
Solvent Atoms180
Heterogen Atoms79

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing