3B1D

Crystal structure of betaC-S lyase from Streptococcus anginosus in complex with L-serine: External aldimine 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
2.2745.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.965α = 90
b = 111.302β = 90
c = 217.193γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 2702008-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.6636.8499.20.0720.0727.914.7189945189945
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)
11.661.798.30.2480.2483.114.613790

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 REPLACEMENTTHROUGHOUT1.6636.8417990317990395291000.152290.152290.150970.1773RANDOM9.178
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]
0.73-0.21-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_4_deg15.596
r_dihedral_angle_3_deg11.627
r_dihedral_angle_1_deg5.842
r_scangle_it3.282
r_scbond_it2.041
r_angle_refined_deg1.318
r_mcangle_it1.178
r_angle_other_deg0.921
r_mcbond_it0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.545
r_dihedral_angle_4_deg15.596
r_dihedral_angle_3_deg11.627
r_dihedral_angle_1_deg5.842
r_scangle_it3.282
r_scbond_it2.041
r_angle_refined_deg1.318
r_mcangle_it1.178
r_angle_other_deg0.921
r_mcbond_it0.62
r_chiral_restr0.242
r_symmetry_vdw_other0.223
r_nbd_refined0.213
r_symmetry_vdw_refined0.197
r_nbd_other0.187
r_nbtor_refined0.18
r_mcbond_other0.169
r_symmetry_hbond_refined0.139
r_xyhbond_nbd_refined0.131
r_nbtor_other0.083
r_metal_ion_refined0.057
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12484
Nucleic Acid Atoms
Solvent Atoms1616
Heterogen Atoms287

Software

Software
Software NamePurpose
SERGUIdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling