X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6298PEG3350, ammonium sulfate, sodium Citrate
Crystal Properties
Matthews coefficientSolvent content
2.5151.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.513α = 74.64
b = 54.792β = 81.94
c = 92.224γ = 89.98
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELRIGAKU HyPic-6000HE2016-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-X1.5406

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
12.218.4499.30.1060.1230.0620.9926.23.440974
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2798.90.5870.760.4760.5652.3

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 REPLACEMENTTHROUGHOUT3VVY2.218.4438659203398.590.22360.21960.2992RANDOM57.627
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]
0.070.16-0.64-1.78-1.170.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg22.584
r_dihedral_angle_3_deg21.509
r_dihedral_angle_1_deg6.58
r_angle_refined_deg1.566
r_angle_other_deg1.321
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.43
r_dihedral_angle_4_deg22.584
r_dihedral_angle_3_deg21.509
r_dihedral_angle_1_deg6.58
r_angle_refined_deg1.566
r_angle_other_deg1.321
r_chiral_restr0.068
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.008
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5848
Nucleic Acid Atoms
Solvent Atoms662
Heterogen Atoms113

Software

Software
Software NamePurpose
Aimlessdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction