1AV6

VACCINIA METHYLTRANSFERASE VP39 COMPLEXED WITH M7G CAPPED RNA HEXAMER AND S-ADENOSYLHOMOCYSTEINE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VPTPDB ENTRY 1VPT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.5pH 8.50
Crystal Properties
Matthews coefficientSolvent content
2.7756

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.8α = 90
b = 64.6β = 90
c = 99.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103AREA DETECTORSIEMENSGOBEL MIRROR1997-08-15M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
12.720920.0952039755227
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)
2.72.80.2162

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULARFREE-RPDB ENTRY 1VPT2.8829284920.2150.2150.285RANDOM13
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_mcangle_it2
x_scbond_it2
x_scangle_it2
x_angle_deg1.7
x_mcbond_it1.5
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
RMS Deviations
KeyRefinement Restraint Deviation
x_mcangle_it2
x_scbond_it2
x_scangle_it2
x_angle_deg1.7
x_mcbond_it1.5
x_bond_d0.01
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d
x_improper_angle_d_na
x_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2387
Nucleic Acid Atoms130
Solvent Atoms
Heterogen Atoms58

Software

Software
Software NamePurpose
AMoREphasing
X-PLORrefinement
SMARTdata reduction
SAINTdata scaling