3ONF

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


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 cordycepin, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2244.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.623α = 90
b = 122.623β = 90
c = 126.622γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-02-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X12EMBL/DESY, HAMBURGX12

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
125099.70.13117.510.565547-322.7
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)
122.071000.6863.19.5

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 FREE1V8B2506572964344111999.80.1570.1560.201RANDOM18.72
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]
-0.11-0.110.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_dihedral_angle_4_deg17.579
r_dihedral_angle_3_deg13.944
r_dihedral_angle_1_deg6.278
r_scangle_it5.427
r_scbond_it3.576
r_angle_refined_deg1.479
r_mcangle_it1.434
r_angle_other_deg1.236
r_mcbond_it0.756
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.935
r_dihedral_angle_4_deg17.579
r_dihedral_angle_3_deg13.944
r_dihedral_angle_1_deg6.278
r_scangle_it5.427
r_scbond_it3.576
r_angle_refined_deg1.479
r_mcangle_it1.434
r_angle_other_deg1.236
r_mcbond_it0.756
r_mcbond_other0.184
r_chiral_restr0.084
r_bond_refined_d0.015
r_gen_planes_refined0.007
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7500
Nucleic Acid Atoms
Solvent Atoms637
Heterogen Atoms134

Software

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