5FJN

Structure of L-Amino acid deaminase from Proteus myxofaciens in complex with anthranilate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5FJMPDB ENTRY 5FJM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.515% PEG 6K, 0.1 M MES (PH 6.5), 10% MPD
Crystal Properties
Matthews coefficientSolvent content
2.4850.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.81α = 90
b = 93.32β = 103.22
c = 75.07γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2015-05-13MSINGLE 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
11.7545.998.10.0314.92.7964091.9
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)
11.751.8497.90.511.92.7

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 5FJM1.7541.1991561481897.940.158420.15640.19669RANDOM36.813
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]
-0.62-0.29-0.10.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.493
r_sphericity_free25.613
r_dihedral_angle_4_deg15.663
r_dihedral_angle_3_deg12.797
r_sphericity_bonded7.811
r_dihedral_angle_1_deg5.474
r_long_range_B_refined3.572
r_long_range_B_other3.459
r_mcangle_it2.996
r_mcangle_other2.996
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.493
r_sphericity_free25.613
r_dihedral_angle_4_deg15.663
r_dihedral_angle_3_deg12.797
r_sphericity_bonded7.811
r_dihedral_angle_1_deg5.474
r_long_range_B_refined3.572
r_long_range_B_other3.459
r_mcangle_it2.996
r_mcangle_other2.996
r_scangle_other2.562
r_mcbond_it2.415
r_mcbond_other2.411
r_scbond_it2.153
r_scbond_other2.153
r_angle_refined_deg1.098
r_rigid_bond_restr1.067
r_angle_other_deg0.736
r_chiral_restr0.059
r_bond_refined_d0.005
r_gen_planes_refined0.004
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6888
Nucleic Acid Atoms
Solvent Atoms542
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing