3PC4

Full length structure of cystathionine beta-synthase from Drosophila in complex with serine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3PC2PDB entry 3PC2

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.529823% PEG 3350, 0.2 Li2SO4, 100 mM BIS-TRIS 6.5, vapor diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.947α = 90
b = 137.935β = 90
c = 75.129γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDK-B pair of biomorph mirrors for vertical and horizontal focusing2009-12-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.9798APS23-ID-D

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
11.75098.90.06311.95.45304852465
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)
11.71.7698.10.4825.35114

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3PC21.741.215308152462266998.860.180.17880.2033RANDOM23.1731
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]
0.82-0.24-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg18.483
r_dihedral_angle_3_deg13.35
r_dihedral_angle_1_deg5.879
r_scangle_it3.279
r_scbond_it1.969
r_mcangle_it1.306
r_angle_refined_deg1.277
r_mcbond_it0.713
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.56
r_dihedral_angle_4_deg18.483
r_dihedral_angle_3_deg13.35
r_dihedral_angle_1_deg5.879
r_scangle_it3.279
r_scbond_it1.969
r_mcangle_it1.306
r_angle_refined_deg1.277
r_mcbond_it0.713
r_chiral_restr0.085
r_bond_refined_d0.011
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3865
Nucleic Acid Atoms
Solvent Atoms598
Heterogen Atoms66

Software

Software
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
PHASERphasing