6A0M

Mandelate oxidase mutant-Y128F with 2-Phenylacetic 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
3.4864.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 138.15α = 90
b = 138.15β = 90
c = 111.217γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker DIP-60402016-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU1SPring-8BL44XU

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
11.753099.90.0370.02135.89.354092
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)
11.751.811000.790.360.76827.8

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 REPLACEMENTTHROUGHOUT3SGZ1.753049594262096.390.163960.162860.18519RANDOM26.095
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]
-0.09-0.090.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.326
r_dihedral_angle_4_deg16.412
r_dihedral_angle_3_deg14.548
r_long_range_B_refined7.728
r_long_range_B_other7.727
r_dihedral_angle_1_deg6.105
r_scangle_other5.7
r_scbond_it3.656
r_scbond_other3.655
r_mcangle_it3.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.326
r_dihedral_angle_4_deg16.412
r_dihedral_angle_3_deg14.548
r_long_range_B_refined7.728
r_long_range_B_other7.727
r_dihedral_angle_1_deg6.105
r_scangle_other5.7
r_scbond_it3.656
r_scbond_other3.655
r_mcangle_it3.47
r_mcangle_other3.469
r_mcbond_it2.32
r_mcbond_other2.32
r_angle_refined_deg1.834
r_angle_other_deg0.881
r_chiral_restr0.113
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms2458
Nucleic Acid Atoms
Solvent Atoms279
Heterogen Atoms41

Software

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