9G1A | pdb_00009g1a

Fragment screening of FosAKP, room-temperature structure, ground state


X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V91 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529125 mg/mL FosAKP in 10 mM Hepes, pH 7.5, 75 mM NaCl was supplemented with 6 mM MnCl2 and mixed with an equal volume of 16% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5 and 1/10 volume of seed stock in 26% (w/v) PEG3350, 0.25 M MgCl2, 0.2 M KBr, 0.1 M BisTris, pH 5.5. From this, approximately 14 uL were added per window of the fixed-target chip. The sample holder was then inserted for into a 3D-printed crystal growth chamber with 3 mL of precipitant solution in the bottom for vapor-diffusion crystallization and incubated at 20C. Before data collection sample holder was removed from the crystal growth chamber and excess precipitant was removed by blotting through the micropores of the membranes, before 10 uL of crystallization solution with 5 % DMSO were pipetted to the crystals in the individual compartments. Sample holders were then placed back into the growths vessel and incubated for 24h. Before data collection blotting was repeated for removal of excess liquid in order to minimize background scattering. Sample holders were then equipped with a protective cover to prevent them from drying-out and stored in a humid atmosphere (figure ??). Compound addition and liquid removal were conducted in a glove box with >95% rel. humidity.
Crystal Properties
Matthews coefficientSolvent content
2.2846.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.62α = 90
b = 91.69β = 90
c = 45.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray296.15PIXELDECTRIS PILATUS 6M-FCRL2023-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, DESY BEAMLINE P09 HiPhaX0.7749PETRA III, DESYP09 HiPhaX

Serial Crystallography

Sample delivery method
Diffraction IDDescriptionSample Delivery Method
1Roadrunner Goniometerfixed target
Fixed Target
Diffraction IDDescriptionSample HoldingSupport BaseMotion controlDetails Sample Solvent
1Kapton with microporesRoadrunner Goniometer
Data Reduction
Diffraction IDFrames IndexedCrystal HitsFrames IndexedLatices Merged
1104856104856

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
11.371.431000.98930.08379.12349.17417516.64
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)
11.31.32299.970.35191.16280.7842.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)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)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.345.851.3373233359398.810.13920.13830.14060.15690.156922.66
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d5.3827
f_angle_d0.8858
f_chiral_restr0.0765
f_plane_restr0.0114
f_bond_d0.0052
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2144
Nucleic Acid Atoms
Solvent Atoms210
Heterogen Atoms2

Software

Software
Software NamePurpose
CrystFELdata reduction
CrystFELdata scaling
PHENIXphasing
PHENIXrefinement
Cootmodel building