6A1A

Mandelate oxidase mutant-Y128F with 4-hydroxymandelic 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
3.564.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.836α = 90
b = 137.836β = 90
c = 111.469γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-07-08MSINGLE 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
11.35301000.0510.0236.0912.2116144
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)
11.351.41000.7460.2690.8442.6912

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 REPLACEMENTTHROUGHOUT3SGZ1.3530106077543595.920.167420.16680.1796RANDOM17.726
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]
-0.05-0.050.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.944
r_dihedral_angle_4_deg14.252
r_dihedral_angle_3_deg12.101
r_long_range_B_refined5.973
r_dihedral_angle_1_deg5.67
r_long_range_B_other5.457
r_scangle_other2.127
r_mcangle_it1.637
r_mcangle_other1.637
r_angle_refined_deg1.381
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.944
r_dihedral_angle_4_deg14.252
r_dihedral_angle_3_deg12.101
r_long_range_B_refined5.973
r_dihedral_angle_1_deg5.67
r_long_range_B_other5.457
r_scangle_other2.127
r_mcangle_it1.637
r_mcangle_other1.637
r_angle_refined_deg1.381
r_scbond_it1.311
r_scbond_other1.31
r_mcbond_it0.954
r_mcbond_other0.951
r_angle_other_deg0.924
r_chiral_restr0.077
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms2498
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms55

Software

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