5XGX

Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M Bis-Tris propane pH 7.0 1 M ammonium citrate tribasic pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.6453.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.878α = 90
b = 107.878β = 90
c = 155.879γ = 90
Symmetry
Space GroupP 4 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPAL/PLS BEAMLINE 5C (4A)0.9796PAL/PLS5C (4A)

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
12.3350.0197.131.86.836407

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 DIFFRACTIONTHROUGHOUT2.3350.0136407191095.880.191770.188860.24636RANDOM39.708
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]
0.720.72-1.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.197
r_dihedral_angle_4_deg24.997
r_dihedral_angle_3_deg15.283
r_long_range_B_refined8.272
r_long_range_B_other8.245
r_dihedral_angle_1_deg7.503
r_scangle_other6.071
r_mcangle_other4.634
r_mcangle_it4.633
r_scbond_it4.038
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.197
r_dihedral_angle_4_deg24.997
r_dihedral_angle_3_deg15.283
r_long_range_B_refined8.272
r_long_range_B_other8.245
r_dihedral_angle_1_deg7.503
r_scangle_other6.071
r_mcangle_other4.634
r_mcangle_it4.633
r_scbond_it4.038
r_scbond_other4.038
r_mcbond_it3.17
r_mcbond_other3.168
r_angle_refined_deg1.84
r_angle_other_deg1.075
r_chiral_restr0.111
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5780
Nucleic Acid Atoms
Solvent Atoms334
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling