8P37

Structure a catalytically inactive mutant of the IMP dehydrogenase related protein GUAB3 from Synechocystis PCC 6803


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QR6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP295SynGUAB3-C222S crystals were grown in the presence of IMP and NAD+ in mother liquor from the condition 2-48 of the commercial screen Morpheus (Molecular Dimensions), which consists of an amino acid mixture (0.02M DL-Glutamic acid monohydrate, 0.02M DL-Alanine, 0.02M Glycine, 0.02M DL-Lysine monohydrochloride, and 0.02M DL-Serine, a precipitant mix (25% (v/v) PEG 500 MME and 12.5 % (w/v) PEG 20000), and 0.1M of a buffer system (Tris-base, Bicine) adjusted at pH 8.5. Initial conditions: Buffer: 10 mM TrisHCl, pH 8.0 Protein concentration = 15 mg/mL Substrate concentration: 3 mM NAD + 3 mM IMP
Crystal Properties
Matthews coefficientSolvent content
2.1342.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.867α = 90
b = 112.867β = 90
c = 54.119γ = 90
Symmetry
Space GroupI 4

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-10-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.979181423454ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.21939.905940.08770.09140.02540.99914.5412.8277746
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.2191.28480.11.5581.62790.46650.681.5111.923886

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.21939.9177746388276.70.17550.17490.1876RANDOM16.64
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]
0.26980.2698-0.5396
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.46
t_omega_torsion4.9
t_angle_deg1.29
t_bond_d0.013
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2753
Nucleic Acid Atoms
Solvent Atoms331
Heterogen Atoms68

Software

Software
Software NamePurpose
BUSTERrefinement
autoPROCdata processing
autoPROCdata processing
Aimlessdata scaling
autoPROCdata processing
XDSdata reduction
PHASERphasing