6A0B

The crystal structure of Mandelate oxidase mutant Y128F with (R)-3,3,3-trifluoro-2-hydroxy-propionic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SGZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729335% Tascimate, 0.1M Bis-Tris propane pH 7.0
Crystal Properties
Matthews coefficientSolvent content
3.4864.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.45α = 90
b = 137.45β = 90
c = 112.471γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2016-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL15A11NSRRCBL15A1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.653099.60.0370.01934.99.664008
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.71000.580.240.8953.39.3

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 REPLACEMENTTHROUGHOUT3SGZ1.653060690324199.410.156260.155360.17275RANDOM18.313
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]
-0.06-0.060.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.99
r_dihedral_angle_4_deg16.83
r_dihedral_angle_3_deg12.686
r_long_range_B_refined7.091
r_long_range_B_other6.518
r_dihedral_angle_1_deg5.892
r_scangle_other5.027
r_scbond_it3.288
r_scbond_other3.277
r_mcangle_it2.418
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.99
r_dihedral_angle_4_deg16.83
r_dihedral_angle_3_deg12.686
r_long_range_B_refined7.091
r_long_range_B_other6.518
r_dihedral_angle_1_deg5.892
r_scangle_other5.027
r_scbond_it3.288
r_scbond_other3.277
r_mcangle_it2.418
r_mcangle_other2.418
r_angle_refined_deg1.983
r_mcbond_it1.667
r_mcbond_other1.644
r_angle_other_deg0.913
r_chiral_restr0.12
r_bond_refined_d0.021
r_gen_planes_refined0.01
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2478
Nucleic Acid Atoms
Solvent Atoms389
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing