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 (pH10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate
Crystal Properties
Matthews coefficientSolvent content
2.5952.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.969α = 90
b = 83.969β = 90
c = 84.011γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2018-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL26B11.000SPring-8BL26B1

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
11.548.491000.0520.0560.020.99918.27.493136
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)
11.51.5399.50.9291.0020.3720.6867.1

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 REPLACEMENTTHROUGHOUT3ELL1.519.888248480899.890.13030.12820.1711RANDOM22.174
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]
0.320.32-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.741
r_dihedral_angle_4_deg17.037
r_dihedral_angle_3_deg10.683
r_dihedral_angle_1_deg6.564
r_rigid_bond_restr1.568
r_angle_refined_deg1.55
r_angle_other_deg1.496
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.741
r_dihedral_angle_4_deg17.037
r_dihedral_angle_3_deg10.683
r_dihedral_angle_1_deg6.564
r_rigid_bond_restr1.568
r_angle_refined_deg1.55
r_angle_other_deg1.496
r_chiral_restr0.07
r_bond_refined_d0.009
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4000
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms244

Software

Software
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing