4YVF

Structure of S-adenosyl-L-homocysteine hydrolase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293HEPES, PEG 4000, 2-propanol, ethyl acetate
Crystal Properties
Matthews coefficientSolvent content
358.94

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.528α = 90
b = 134.15β = 90
c = 185.164γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93IMAGE PLATERIGAKU RAXIS V2003-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL24XU0.82565SPring-8BL24XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.75099.625.46.183160522.1

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 DIFFRACTIONTHROUGHOUT2.747.8131525156599.50.1990.1990.239RANDOM23.9
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]
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it2.66
c_scbond_it1.85
c_mcangle_it1.6
c_angle_deg1.2
c_mcbond_it1
c_improper_angle_d0.73
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d22
c_scangle_it2.66
c_scbond_it1.85
c_mcangle_it1.6
c_angle_deg1.2
c_mcbond_it1
c_improper_angle_d0.73
c_bond_d0.006
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6644
Nucleic Acid Atoms
Solvent Atoms244
Heterogen Atoms164

Software

Software
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing