3LQS

Complex Structure of D-Amino Acid Aminotransferase and 4-amino-4,5-dihydro-thiophenecarboxylic acid (ADTA)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.5298Crystals were grown by the hanging drop method . The enzyme was dialyzed in 0.2 M potassium phosphate buffer pH 7.2, concentrated to 40mg/mL, and incubated with an R-ADTA:protein molecular ratio of 200:1 prior to crystallization. The enzyme solution was mixed with crystallization buffer at pH 8.5 and incubated initially at 30-40 C, then allowed to return to room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.011α = 90
b = 90.728β = 90
c = 88.893γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200IMAGE PLATERIGAKU RAXIS IVMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.963.597.414.9448439
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)
11.91.97950.5092.54660

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.963.545930246597.290.162340.160520.19585RANDOM23.108
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]
0.081.02-1.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.436
r_dihedral_angle_3_deg15.003
r_dihedral_angle_4_deg14.494
r_dihedral_angle_1_deg5.33
r_scangle_it4.277
r_scbond_it2.71
r_angle_refined_deg1.764
r_mcangle_it1.649
r_mcbond_it1.009
r_symmetry_vdw_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.436
r_dihedral_angle_3_deg15.003
r_dihedral_angle_4_deg14.494
r_dihedral_angle_1_deg5.33
r_scangle_it4.277
r_scbond_it2.71
r_angle_refined_deg1.764
r_mcangle_it1.649
r_mcbond_it1.009
r_symmetry_vdw_refined0.323
r_nbtor_refined0.307
r_nbd_refined0.198
r_symmetry_hbond_refined0.198
r_xyhbond_nbd_refined0.122
r_chiral_restr0.106
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4514
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing