8JSZ

Crystal structure of a uridylate cyclase from Anabaena sp.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2770.1 M BIS-TRIS pH 6.5, 0.2 M Magnesium chloride hexahydrate, 25% w/v Polyethylene glycol 3,350
Crystal Properties
Matthews coefficientSolvent content
2.2545.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.661α = 71.21
b = 50.792β = 83.96
c = 71.391γ = 62.07
Symmetry
Space GroupP 1

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
11.833097.60.99827.55.547377
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)
11.841.9195.10.9725.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTAlphaFold1.8325.05250402227796.570.177650.176510.17893RANDOM21.504
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]
-0.080.160.09-0.24-0.260.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.829
r_dihedral_angle_4_deg19.667
r_dihedral_angle_3_deg13.744
r_long_range_B_other8.982
r_long_range_B_refined8.962
r_scangle_other8.101
r_scbond_it6.351
r_scbond_other6.349
r_dihedral_angle_1_deg6.171
r_mcangle_it5.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.829
r_dihedral_angle_4_deg19.667
r_dihedral_angle_3_deg13.744
r_long_range_B_other8.982
r_long_range_B_refined8.962
r_scangle_other8.101
r_scbond_it6.351
r_scbond_other6.349
r_dihedral_angle_1_deg6.171
r_mcangle_it5.986
r_mcangle_other5.986
r_mcbond_it4.749
r_mcbond_other4.699
r_angle_other_deg2.225
r_angle_refined_deg1.731
r_chiral_restr0.097
r_bond_other_d0.034
r_bond_refined_d0.014
r_gen_planes_other0.005
r_gen_planes_refined0.004
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 Atoms4168
Nucleic Acid Atoms
Solvent Atoms648
Heterogen Atoms24

Software

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