6PS6

XFEL beta2 AR structure by ligand exchange from Timolol to Timolol.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3D4S 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE2930.1 M HEPES pH 7.0, 0.1 M Ammonium Sulfate, 30% PEG 400, 2 mM of target ligand Timolol
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.48α = 90
b = 76.19β = 90
c = 171.96γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCS-PAD CXI-12014-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.33SLAC LCLSCXI

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1injection
Injection
Diffraction IDDescriptionFlow RateInjector DiameterInjection PowerInjector NozzleFilter SizeCarrier Solvent
10.2
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
1421201.59.5
Data Reduction
Diffraction IDFrames IndexedCrystal HitsTotal Frames
11795280792918091

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)R Split (All)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
12.731.41000.9860.1774.2170.915738
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.890.2461.855

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 REPLACEMENTTHROUGHOUT3d4s2.731.351566578599.80.2180.2180.232RANDOM87.5
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]
-11.98325.80436.1788
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.95
t_omega_torsion2.01
t_angle_deg0.96
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion2.95
t_omega_torsion2.01
t_angle_deg0.96
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3478
Nucleic Acid Atoms
Solvent Atoms10
Heterogen Atoms226

Software

Software
Software NamePurpose
PHASERphasing
BUSTERrefinement
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling