X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H4E 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290PEG550MME (13-14%), KSCN (0.15M), TRIS (0.1M, pH 8.5)
Crystal Properties
Matthews coefficientSolvent content
2.9257.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.69α = 90
b = 159.27β = 90
c = 249.399γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2014-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.119.9997.40.0940.0650.9867.12.831869
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.27920.5520.4110.6511.92.44366

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 REPLACEMENTTHROUGHOUT3H4E3.119.9930312155296.870.25170.25010.2819RANDOM108.434
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]
0.54-3.643.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.265
r_dihedral_angle_3_deg12.882
r_dihedral_angle_4_deg10.298
r_mcangle_it8.518
r_dihedral_angle_1_deg6.228
r_mcbond_it5.3
r_mcbond_other5.299
r_angle_refined_deg1.166
r_angle_other_deg1.024
r_chiral_restr0.056
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.265
r_dihedral_angle_3_deg12.882
r_dihedral_angle_4_deg10.298
r_mcangle_it8.518
r_dihedral_angle_1_deg6.228
r_mcbond_it5.3
r_mcbond_other5.299
r_angle_refined_deg1.166
r_angle_other_deg1.024
r_chiral_restr0.056
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.004
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9316
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms193

Software

Software
Software NamePurpose
MAR345dtbdata collection
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction