6C2Q

Crystal Structures of Cystathionine beta-Synthase from Saccharomyces cerevisiae: the Structure of the PLP-L-Serine 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 DROP827730% PEG400, 100 mM calcium acetate, 100 mM Tris, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.6152.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.107α = 90
b = 81.107β = 90
c = 208.519γ = 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
12.17501000.0630.0660.01912.411.222476
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.172.211000.2770.2920.0930.9879.5

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 1JBQ2.175021199119599.840.16130.1590.2025RANDOM31.347
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]
0.180.090.18-0.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.515
r_dihedral_angle_4_deg13.045
r_dihedral_angle_3_deg12.395
r_dihedral_angle_1_deg6.044
r_angle_refined_deg1.389
r_angle_other_deg0.935
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.515
r_dihedral_angle_4_deg13.045
r_dihedral_angle_3_deg12.395
r_dihedral_angle_1_deg6.044
r_angle_refined_deg1.389
r_angle_other_deg0.935
r_chiral_restr0.082
r_bond_refined_d0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2675
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms71

Software

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