8S2W

SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7NHF 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE7294600 mM Sodium citrate and 100 mM HEPES pH 7
Crystal Properties
Matthews coefficientSolvent content
2.8657.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.9α = 90
b = 177.9β = 90
c = 117.3γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELPSI JUNGFRAU 4M2023-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID291.07ESRFID29

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1SOS Chipfixed target
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
1193252026819325

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
12.593.331000.964.447.44787849.36
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.541000.170.545.18

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.564.47247873231699.9940.1690.16760.1934RANDOM59.434
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]
-0.005-0.002-0.0050.016
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.18
r_dihedral_angle_6_deg14.129
r_lrange_other11.013
r_lrange_it11.006
r_scangle_it9.179
r_scangle_other9.099
r_dihedral_angle_2_deg7.892
r_mcangle_it6.57
r_mcangle_other6.57
r_dihedral_angle_1_deg6.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.18
r_dihedral_angle_6_deg14.129
r_lrange_other11.013
r_lrange_it11.006
r_scangle_it9.179
r_scangle_other9.099
r_dihedral_angle_2_deg7.892
r_mcangle_it6.57
r_mcangle_other6.57
r_dihedral_angle_1_deg6.304
r_scbond_it5.847
r_scbond_other5.714
r_mcbond_it4.34
r_mcbond_other4.339
r_angle_refined_deg1.407
r_angle_other_deg0.458
r_nbd_refined0.213
r_symmetry_nbd_other0.199
r_nbtor_refined0.173
r_symmetry_nbd_refined0.157
r_nbd_other0.152
r_symmetry_xyhbond_nbd_refined0.141
r_xyhbond_nbd_refined0.135
r_symmetry_nbtor_other0.082
r_ncsr_local_group_50.07
r_ncsr_local_group_60.07
r_ncsr_local_group_30.064
r_chiral_restr0.062
r_ncsr_local_group_10.062
r_ncsr_local_group_20.061
r_ncsr_local_group_40.059
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms8056
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata reduction
CrystFELdata scaling
MOLREPphasing