2PXA

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.62930.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 30 % w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2344.83

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.423α = 90
b = 80.28β = 90
c = 84.814γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102006-03-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.93400ESRFID14-1

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
12.3301000.09132.613.824920-1.5
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)
12.32.41000.6623.49.72426

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 2PX22.33023377122299.90.190590.187630.24576RANDOM34.26
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]
0.48-0.38-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.493
r_dihedral_angle_3_deg14.704
r_dihedral_angle_4_deg14.445
r_scangle_it8.719
r_scbond_it6.499
r_mcangle_it4.975
r_dihedral_angle_1_deg4.912
r_mcbond_it4.299
r_angle_refined_deg1.246
r_mcbond_other1.209
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.493
r_dihedral_angle_3_deg14.704
r_dihedral_angle_4_deg14.445
r_scangle_it8.719
r_scbond_it6.499
r_mcangle_it4.975
r_dihedral_angle_1_deg4.912
r_mcbond_it4.299
r_angle_refined_deg1.246
r_mcbond_other1.209
r_angle_other_deg0.813
r_symmetry_vdw_other0.255
r_nbd_refined0.196
r_nbd_other0.188
r_nbtor_refined0.176
r_symmetry_hbond_refined0.168
r_xyhbond_nbd_refined0.138
r_symmetry_vdw_refined0.123
r_nbtor_other0.083
r_chiral_restr0.066
r_bond_refined_d0.009
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 Atoms4164
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms116

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing