X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529340% (w/v) PEG3350, 10 mM L-Asn, and 0.17 M sodium citrate
Crystal Properties
Matthews coefficientSolvent content
2.0740.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.342α = 90
b = 62.538β = 117.68
c = 141.299γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4MMultilayer X-ray mirrors VariMax HF2018-06-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.954098.30.0660.0440.91215.73.184238
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)
11.951.980.5140.4230.6711.72

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 REPLACEMENTTHROUGHOUT3eca1.9527.979550401897.630.1440.14180.1863RANDOM26.443
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]
-0.240.28-0.450.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.005
r_dihedral_angle_4_deg18.484
r_dihedral_angle_3_deg14.94
r_dihedral_angle_1_deg6.627
r_angle_refined_deg1.864
r_angle_other_deg1.079
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.005
r_dihedral_angle_4_deg18.484
r_dihedral_angle_3_deg14.94
r_dihedral_angle_1_deg6.627
r_angle_refined_deg1.864
r_angle_other_deg1.079
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9768
Nucleic Acid Atoms
Solvent Atoms1223
Heterogen Atoms56

Software

Software
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing