5H8L

Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) C158S mutant in complex with putrescine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729220% PEG3350, 8% Tacsimate at pH 7.0, 10% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.0759.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 152.21α = 90
b = 211.082β = 90
c = 208.613γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300-HS2015-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.000APS22-ID

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
12.294097.50.1188.683.79294391-3
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)
12.292.42880.6151.973.78

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 REPLACEMENTFREE R-VALUE1ERZ2.2939.53291447294497.50.1550.1540.206RANDOM46.7
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]
-1.421.64-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.87
r_dihedral_angle_4_deg17.926
r_dihedral_angle_3_deg14.015
r_long_range_B_refined8.404
r_long_range_B_other8.404
r_dihedral_angle_1_deg5.973
r_scangle_other3.973
r_scbond_it2.702
r_scbond_other2.697
r_mcangle_it2.568
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.87
r_dihedral_angle_4_deg17.926
r_dihedral_angle_3_deg14.015
r_long_range_B_refined8.404
r_long_range_B_other8.404
r_dihedral_angle_1_deg5.973
r_scangle_other3.973
r_scbond_it2.702
r_scbond_other2.697
r_mcangle_it2.568
r_mcangle_other2.568
r_mcbond_it1.667
r_mcbond_other1.667
r_angle_refined_deg1.6
r_angle_other_deg0.796
r_chiral_restr0.118
r_gen_planes_refined0.02
r_bond_refined_d0.017
r_gen_planes_other0.015
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms37559
Nucleic Acid Atoms
Solvent Atoms3705
Heterogen Atoms341

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
BALBESphasing