X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP10.5293100mM CAPS/NaOH (pH 10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.6854.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.06α = 90
b = 85.06β = 90
c = 84.087γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225-HS2018-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000SPring-8BL26B2

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
11.5548.921000.070.0730.01912214.986763
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)
11.551.581001.6261.7010.4930.58911.8

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 REPLACEMENTTHROUGHOUT3ELL1.552082230445099.910.13310.13150.1635RANDOM24.251
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]
0.290.29-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.954
r_dihedral_angle_4_deg17.473
r_dihedral_angle_3_deg9.992
r_dihedral_angle_1_deg6.375
r_rigid_bond_restr1.61
r_angle_other_deg1.438
r_angle_refined_deg1.43
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.006
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.954
r_dihedral_angle_4_deg17.473
r_dihedral_angle_3_deg9.992
r_dihedral_angle_1_deg6.375
r_rigid_bond_restr1.61
r_angle_other_deg1.438
r_angle_refined_deg1.43
r_chiral_restr0.063
r_bond_refined_d0.008
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3969
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms245

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing