2VD6

Human adenylosuccinate lyase in complex with its substrate N6-(1,2- Dicarboxyethyl)-AMP, and its products AMP and fumarate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2J91PDB ENTRY 2J91

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.4148.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 87.3α = 90
b = 128.1β = 90
c = 190.5γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2006-05-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
122599.70.0621.37.2144136
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)
122.299.80.385.57.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2J91250136929720799.80.1940.1920.229RANDOM28.83
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]
1.790.08-1.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg13.61
r_dihedral_angle_1_deg5.263
r_scangle_it1.717
r_scbond_it1.165
r_angle_refined_deg1.088
r_angle_other_deg0.877
r_mcangle_it0.648
r_mcbond_it0.567
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg13.61
r_dihedral_angle_1_deg5.263
r_scangle_it1.717
r_scbond_it1.165
r_angle_refined_deg1.088
r_angle_other_deg0.877
r_mcangle_it0.648
r_mcbond_it0.567
r_symmetry_vdw_refined0.3
r_symmetry_vdw_other0.247
r_nbd_refined0.199
r_nbd_other0.181
r_nbtor_refined0.171
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.136
r_nbtor_other0.083
r_chiral_restr0.058
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_gen_planes_other0.002
r_bond_other_d0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14706
Nucleic Acid Atoms
Solvent Atoms880
Heterogen Atoms161

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing