9EPJ | pdb_00009epj

DtpAa Y389F 41 fs 10 microjoules XFEL Pulse Data Collection


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6I43 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH MODE29812% v/v PEG 3350, 100 mM HEPES pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.72α = 90
b = 68.2β = 105.6
c = 74.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray294.15PIXELPSI JUNGFRAU 8M2023-09-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSwissFEL ARAMIS BEAMLINE ESA1.03SwissFEL ARAMISESA

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1fixed target
Measurement
Diffraction IDPulse DurationPulse Repetition RateFocal Spot SizePulse EnergyPhotons Per Pulse
136 (fs)undefined (KeV)

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
11.3834.121000.9174.05115.7147332
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)
11.381.411000.3761.02

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.3834.12137006712799.980.171590.170420.17370.194230.1755RANDOM17.971
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]
0.25-0.05-0.330.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.797
r_dihedral_angle_2_deg8.35
r_dihedral_angle_1_deg6.365
r_long_range_B_refined5.788
r_long_range_B_other5.739
r_scangle_other4.688
r_scbond_other3.021
r_scbond_it3.02
r_mcangle_other2.448
r_mcangle_it2.447
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg11.797
r_dihedral_angle_2_deg8.35
r_dihedral_angle_1_deg6.365
r_long_range_B_refined5.788
r_long_range_B_other5.739
r_scangle_other4.688
r_scbond_other3.021
r_scbond_it3.02
r_mcangle_other2.448
r_mcangle_it2.447
r_angle_refined_deg1.813
r_mcbond_it1.675
r_mcbond_other1.673
r_angle_other_deg0.619
r_chiral_restr0.093
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_gen_planes_other0.005
r_bond_other_d0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5544
Nucleic Acid Atoms
Solvent Atoms535
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
CrystFELdata scaling
CrystFELdata reduction
Cootmodel building
REFMACphasing