3N58

Crystal structure of S-ADENOSYL-L-HOMOCYSTEINE hydrolase from brucella melitensis in ternary complex with NAD and adenosine, orthorhombic form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ZIZPDB entry 2ZIZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8290JCSG SCREEN CONDITION D12: 20% V/ V GLYCEROL, 16% W/V PEG 8000, 40 MM POTASSIUM PHOSPHATE, PROTEIN AT 80 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.5852.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.45α = 90
b = 165.23β = 90
c = 184.14γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102010-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.10.97740ALS5.0.1

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
12.3949.271000.10916.097.78356783542-334.18
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)
12.392.451000.5223.676114

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONPDB entry 2ZIZ2.3949.27835678354239870.1750.1750.1720.235RANDOM32.99
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]
14.175-6.972-7.566
RMS Deviations
KeyRefinement Restraint Deviation
f_angle_d1.192
f_bond_d0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13850
Nucleic Acid Atoms
Solvent Atoms712
Heterogen Atoms236

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling