3FDB

Crystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from corynebacterium diphtheriae at 1.99 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52770.2000M MgCl2, 10.0000% PEG-3000, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5164.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.18α = 90
b = 69.18β = 90
c = 215.46γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDFlat collimating mirror, toroid focusing mirror2008-08-03MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.91837,0.97934,0.97922SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.9929.96199.10.06110.7747285-330.512
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.911.9898.50.731.5

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 DIFFRACTIONMADTHROUGHOUT1.9929.96141858214099.430.1490.1470.175RANDOM43.667
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]
2.281.142.28-3.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.315
r_dihedral_angle_4_deg12.891
r_dihedral_angle_3_deg11.185
r_scangle_it7.027
r_scbond_it5.015
r_dihedral_angle_1_deg4.65
r_mcangle_it2.525
r_mcbond_it1.579
r_angle_refined_deg1.471
r_angle_other_deg0.967
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.315
r_dihedral_angle_4_deg12.891
r_dihedral_angle_3_deg11.185
r_scangle_it7.027
r_scbond_it5.015
r_dihedral_angle_1_deg4.65
r_mcangle_it2.525
r_mcbond_it1.579
r_angle_refined_deg1.471
r_angle_other_deg0.967
r_mcbond_other0.48
r_symmetry_vdw_other0.272
r_symmetry_hbond_refined0.248
r_symmetry_vdw_refined0.233
r_nbd_refined0.213
r_metal_ion_refined0.198
r_nbd_other0.196
r_nbtor_refined0.184
r_xyhbond_nbd_refined0.182
r_chiral_restr0.095
r_nbtor_other0.091
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2950
Nucleic Acid Atoms
Solvent Atoms431
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing