2PX5

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.2 M Magnesium sulfate, 20 % w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.9α = 90
b = 89.1β = 90
c = 101.9γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDmirrors2005-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97625ESRFBM14

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
12.33095.90.12312.36.227379-1.5
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)
12.32.481.30.4362.34.52276

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 2PX22.320.1225651132896.070.190350.186810.2601RANDOM48.621
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]
-0.871.66-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.137
r_dihedral_angle_4_deg15.742
r_dihedral_angle_3_deg15.419
r_scangle_it8.974
r_scbond_it7.214
r_mcangle_it5.258
r_dihedral_angle_1_deg4.868
r_mcbond_it4.647
r_mcbond_other1.376
r_angle_refined_deg1.147
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.137
r_dihedral_angle_4_deg15.742
r_dihedral_angle_3_deg15.419
r_scangle_it8.974
r_scbond_it7.214
r_mcangle_it5.258
r_dihedral_angle_1_deg4.868
r_mcbond_it4.647
r_mcbond_other1.376
r_angle_refined_deg1.147
r_angle_other_deg0.84
r_symmetry_hbond_refined0.237
r_nbd_other0.192
r_nbd_refined0.19
r_nbtor_refined0.177
r_xyhbond_nbd_refined0.172
r_symmetry_vdw_other0.167
r_symmetry_vdw_refined0.162
r_nbtor_other0.083
r_chiral_restr0.059
r_bond_refined_d0.01
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4181
Nucleic Acid Atoms
Solvent Atoms335
Heterogen Atoms97

Software

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