3OND

Crystal structure of Lupinus luteus S-adenosyl-L-homocysteine hydrolase in complex with adenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1V8B 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829220% PEG 4000, 10% isopropanol, 0.1 M Tris-HCl pH 8.0, 2 mM adenosine, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2144.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.417α = 90
b = 122.417β = 90
c = 126.571γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2007-12-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.172099.90.05738.310.7319469-39.9
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)
11.171.1998.50.7082.35.3

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 REPLACEMENTR FREE1V8B1.1720319641315006109398.90.1280.1280.159RANDOM11.94
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]
-0.13-0.130.27
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg16.458
r_dihedral_angle_3_deg12.702
r_sphericity_free9.999
r_dihedral_angle_1_deg6.595
r_scangle_it5.564
r_sphericity_bonded5.036
r_scbond_it4.085
r_mcangle_it2.643
r_angle_refined_deg1.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.264
r_dihedral_angle_4_deg16.458
r_dihedral_angle_3_deg12.702
r_sphericity_free9.999
r_dihedral_angle_1_deg6.595
r_scangle_it5.564
r_sphericity_bonded5.036
r_scbond_it4.085
r_mcangle_it2.643
r_angle_refined_deg1.926
r_rigid_bond_restr1.905
r_mcbond_it1.881
r_angle_other_deg1.232
r_mcbond_other0.968
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7516
Nucleic Acid Atoms
Solvent Atoms1493
Heterogen Atoms152

Software

Software
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling