9EQT | pdb_00009eqt

24fs pulse duration 10uJ pulse energy thaumatin


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4AXR 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE293100 mg of thaumatin (Sigma-T7638) was dissolved in 1 ml of MiniQ water, reaching a concentration of 100 mg/ml with solutions vortexed to ensure complete dissolution. Subsequently, 200 uL of the thaumatin solution was mixed with 200 ul of 1.6 M (Na, K, tartrate) crystallization solution
Crystal Properties
Matthews coefficientSolvent content
2.9157.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.5α = 90
b = 58.5β = 90
c = 151.25γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELPSI JUNGFRAU 8M2023-09-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESC1.0306SwissFEL ARAMISESC

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlDetails Sample Solvent
1polymer fixed target
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
124 (fs)1007.9812.03 (KeV)
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
11230512305

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
11.49321000.9480.1734.65116.144873
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)
11.491.520.31.356

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.493244772225899.9670.1790.17760.17680.20680.206121.982
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]
0.3150.315-0.629
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.195
r_dihedral_angle_3_deg11.872
r_dihedral_angle_2_deg11.344
r_dihedral_angle_1_deg6.986
r_lrange_it6.538
r_lrange_other6.435
r_scangle_it5.196
r_scangle_other5.196
r_scbond_other3.431
r_scbond_it3.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg16.195
r_dihedral_angle_3_deg11.872
r_dihedral_angle_2_deg11.344
r_dihedral_angle_1_deg6.986
r_lrange_it6.538
r_lrange_other6.435
r_scangle_it5.196
r_scangle_other5.196
r_scbond_other3.431
r_scbond_it3.429
r_mcangle_other3.083
r_mcangle_it3.072
r_mcbond_it2.093
r_mcbond_other2.045
r_angle_refined_deg1.753
r_angle_other_deg0.613
r_xyhbond_nbd_refined0.227
r_nbd_refined0.215
r_symmetry_nbd_other0.202
r_symmetry_nbd_refined0.198
r_nbtor_refined0.188
r_nbd_other0.161
r_symmetry_xyhbond_nbd_refined0.112
r_chiral_restr0.092
r_symmetry_nbtor_other0.088
r_bond_refined_d0.01
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1545
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing