6F7W

Crystal structure of dimethylated RSL - cucurbit[7]uril complex, C2221 Form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2BT92bt9 chain A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29320% PEG 3350 200 mM Sodium Malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.7655.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.343α = 90
b = 87.176β = 90
c = 146.595γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152017-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.9791APS24-ID-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.2843.6950.050.0220.9918.84.578616
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.281.392.40.5010.380.7061.94

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 REPLACEMENTTHROUGHOUT2bt9 chain A1.2843.674734386594.490.12490.12360.1508RANDOM18.503
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]
-0.361.05-0.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_sphericity_free28.573
r_sphericity_bonded9.865
r_dihedral_angle_3_deg9.62
r_dihedral_angle_1_deg6.651
r_dihedral_angle_4_deg3.735
r_rigid_bond_restr1.455
r_angle_refined_deg1.328
r_angle_other_deg1.011
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.493
r_sphericity_free28.573
r_sphericity_bonded9.865
r_dihedral_angle_3_deg9.62
r_dihedral_angle_1_deg6.651
r_dihedral_angle_4_deg3.735
r_rigid_bond_restr1.455
r_angle_refined_deg1.328
r_angle_other_deg1.011
r_chiral_restr0.085
r_gen_planes_refined0.015
r_bond_refined_d0.009
r_bond_other_d0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2070
Nucleic Acid Atoms
Solvent Atoms385
Heterogen Atoms301

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction