6C2Z

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-Aminoacrylate Intermediate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1JBQPDB entry 1JBQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.527730% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.6453.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.465α = 90
b = 81.465β = 90
c = 209.486γ = 120
Symmetry
Space GroupP 65 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-06-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97929APS19-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.375099.60.1040.1070.0257.120.186357
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.371.3999.50.3520.8612.6

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 REPLACEMENTTHROUGHOUTPDB entry 1JBQ1.375075277407291.550.13550.1340.1631RANDOM18.638
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]
-0.02-0.01-0.020.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.04
r_sphericity_free26.327
r_dihedral_angle_4_deg13.473
r_dihedral_angle_3_deg11.676
r_sphericity_bonded11.242
r_dihedral_angle_1_deg6.058
r_rigid_bond_restr1.909
r_angle_refined_deg1.585
r_angle_other_deg0.988
r_chiral_restr0.098
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.04
r_sphericity_free26.327
r_dihedral_angle_4_deg13.473
r_dihedral_angle_3_deg11.676
r_sphericity_bonded11.242
r_dihedral_angle_1_deg6.058
r_rigid_bond_restr1.909
r_angle_refined_deg1.585
r_angle_other_deg0.988
r_chiral_restr0.098
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.003
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2675
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms76

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXphasing
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction