3B1E

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: alpha-Aminoacrylate form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529322% PEG 8000, 0.1M Hepes pH7.5, 0.08M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.204α = 90
b = 111.212β = 90
c = 217.353γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 3152009-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

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
11.7872.3599.80.0960.0966.114.1156276156276
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)
11.781.831000.2380.238314.111457

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.7849.2714799614799678001000.143910.143910.142180.17683RANDOM9.262
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]
1.03-0.72-0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg11.763
r_dihedral_angle_1_deg5.962
r_scangle_it3.502
r_scbond_it2.129
r_angle_refined_deg1.357
r_mcangle_it1.237
r_angle_other_deg0.947
r_mcbond_it0.652
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.298
r_dihedral_angle_4_deg19.272
r_dihedral_angle_3_deg11.763
r_dihedral_angle_1_deg5.962
r_scangle_it3.502
r_scbond_it2.129
r_angle_refined_deg1.357
r_mcangle_it1.237
r_angle_other_deg0.947
r_mcbond_it0.652
r_chiral_restr0.246
r_nbd_refined0.21
r_nbd_other0.188
r_symmetry_vdw_refined0.184
r_mcbond_other0.181
r_nbtor_refined0.179
r_symmetry_vdw_other0.179
r_symmetry_hbond_refined0.13
r_xyhbond_nbd_refined0.129
r_nbtor_other0.083
r_metal_ion_refined0.075
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
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 Atoms12466
Nucleic Acid Atoms
Solvent Atoms1701
Heterogen Atoms257

Software

Software
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling