2X5D

Crystal Structure of a probable aminotransferase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DOUPDB ENTRY 2DOU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1635.9% PEG400, 0.19M LITHIUM SULFATE, 0.1M MES PH6.0. CRYSTAL WAS CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH PLP.
Crystal Properties
Matthews coefficientSolvent content
2.244.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.86α = 90
b = 173.81β = 114.51
c = 76.97γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMIRRORS2008-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
12.328.999.20.121.53.766956
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)
12.32.3697.70.742.923.6

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 2DOU2.2528.8966956366293.360.217530.216060.24422RANDOM2.692
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]
19.1212.98-14.89-4.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_4_deg17.574
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg6
r_scangle_it1.668
r_angle_refined_deg1.357
r_scbond_it1.04
r_angle_other_deg0.9
r_mcangle_it0.535
r_mcbond_it0.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.553
r_dihedral_angle_4_deg17.574
r_dihedral_angle_3_deg15.573
r_dihedral_angle_1_deg6
r_scangle_it1.668
r_angle_refined_deg1.357
r_scbond_it1.04
r_angle_other_deg0.9
r_mcangle_it0.535
r_mcbond_it0.287
r_chiral_restr0.076
r_mcbond_other0.051
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
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_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 Atoms11707
Nucleic Acid Atoms
Solvent Atoms285
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing