3L2B

Crystal structure of the CBS and DRTGG domains of the regulatory region of Clostridium perfringens pyrophosphatase complexed with activator, diadenosine tetraphosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3L31 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.529825% PEG 4000, 100mM Tris/HCl pH 8.5, 200mM LiSO4, 0.25mM Ap4A, vapor diffusion, hanging drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4750.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.847α = 90
b = 71.764β = 90
c = 116.334γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC Quantum Q315r2008-04-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.979260ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)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
12.272098.80.0530.05319.7872455424554-355.681
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.312.4495.50.3740.3744.66.93736

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 REPLACEMENTTHROUGHOUT3L312.2719.9923255129897.240.211230.208650.25875RANDOM45.19
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]
4.48-1.22-3.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.399
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg14.524
r_dihedral_angle_1_deg5.995
r_scangle_it3.193
r_scbond_it2.042
r_mcangle_it1.347
r_angle_refined_deg1.341
r_angle_other_deg1.219
r_mcbond_it0.716
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.399
r_dihedral_angle_4_deg20.855
r_dihedral_angle_3_deg14.524
r_dihedral_angle_1_deg5.995
r_scangle_it3.193
r_scbond_it2.042
r_mcangle_it1.347
r_angle_refined_deg1.341
r_angle_other_deg1.219
r_mcbond_it0.716
r_mcbond_other0.133
r_chiral_restr0.073
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3551
Nucleic Acid Atoms
Solvent Atoms74
Heterogen Atoms53

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
XDSdata reduction