X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VXN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293200mM sodium nitrate, 20%PEG3350
Crystal Properties
Matthews coefficientSolvent content
2.5351.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.714α = 90
b = 87.02β = 90
c = 152.227γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2011-10-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.297509314.064.137537

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 REPLACEMENTTHROUGHOUT3VXN2.2975035649187491.710.22480.22150.287RANDOM46.112
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]
1.8-0.3-1.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.391
r_dihedral_angle_3_deg20.985
r_dihedral_angle_4_deg20.824
r_dihedral_angle_1_deg7.174
r_angle_refined_deg1.114
r_chiral_restr0.09
r_gen_planes_refined0.008
r_bond_refined_d0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6250
Nucleic Acid Atoms
Solvent Atoms227
Heterogen Atoms

Software

Software
Software NamePurpose
SCALEPACKdata reduction
MOLREPmodel building
REFMACrefinement
PDB_EXTRACTdata extraction