8JSK

Crystal structure of an N-terminal cyclic nucleotide-binding domain of a PycTIR from Pseudovibrio sp. in complex with cUMP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.075 M HEPES pH 7.5, 7.5% w/v polyethylene glycol 8,000, 6% v/v ethylene glycol and 25% v/v glycerol
Crystal Properties
Matthews coefficientSolvent content
2.1342.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.485α = 90
b = 133.485β = 90
c = 34.069γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2022-09-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE TPS 07A0.97626NSRRCTPS 07A

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
12.4013099.8123.610.512049
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)
12.412.51000.8082.711

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAlphaFold2.40125.0821195366498.8260.20.19790.243637.905
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]
0.0340.034-0.069
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_3_deg20.089
r_dihedral_angle_4_deg17.812
r_dihedral_angle_1_deg7.672
r_lrange_it7.324
r_lrange_other7.324
r_scangle_it5.203
r_scangle_other5.202
r_mcangle_it4.297
r_mcangle_other4.297
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.703
r_dihedral_angle_3_deg20.089
r_dihedral_angle_4_deg17.812
r_dihedral_angle_1_deg7.672
r_lrange_it7.324
r_lrange_other7.324
r_scangle_it5.203
r_scangle_other5.202
r_mcangle_it4.297
r_mcangle_other4.297
r_scbond_it3.194
r_scbond_other3.193
r_mcbond_it2.808
r_mcbond_other2.806
r_angle_refined_deg1.33
r_angle_other_deg1.149
r_symmetry_xyhbond_nbd_refined0.218
r_nbd_refined0.201
r_symmetry_nbd_refined0.201
r_nbd_other0.196
r_symmetry_nbd_other0.193
r_xyhbond_nbd_refined0.156
r_nbtor_refined0.145
r_symmetry_nbtor_other0.077
r_xyhbond_nbd_other0.077
r_chiral_restr0.052
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2498
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms20

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing