X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5VGI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
Crystal Properties
Matthews coefficientSolvent content
2.5251.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.457α = 90
b = 101.739β = 99.51
c = 142.287γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 3152012-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-D0.95APS14-BM-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.34140.3398.70.10212.33.867709
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.342.480.755

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 REPLACEMENTTHROUGHOUT5VGI2.34140.364243344298.660.17710.1740.2335RANDOM43.884
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]
-0.550.730.10.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg17.826
r_dihedral_angle_1_deg6.863
r_angle_refined_deg1.763
r_angle_other_deg1.06
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.274
r_dihedral_angle_4_deg18.08
r_dihedral_angle_3_deg17.826
r_dihedral_angle_1_deg6.863
r_angle_refined_deg1.763
r_angle_other_deg1.06
r_chiral_restr0.103
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11267
Nucleic Acid Atoms
Solvent Atoms508
Heterogen Atoms92

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing