5ZZR

The crystal structure of Mandelate oxidase with (S)-mandelic 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
3.4764.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.702α = 90
b = 137.702β = 90
c = 111.621γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX300HE2017-07-28MSINGLE 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)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
11.3130990.03734.59.8126061
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)
11.311.361000.6692.49.5

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 REPLACEMENTTHROUGHOUT3SGZ1.3130112497593892.950.166870.166330.17708RANDOM18.28
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]
-0.06-0.060.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.727
r_dihedral_angle_4_deg13.56
r_dihedral_angle_3_deg11.98
r_dihedral_angle_1_deg5.8
r_long_range_B_refined5.639
r_long_range_B_other4.925
r_scangle_other2.486
r_mcangle_other1.859
r_mcangle_it1.857
r_scbond_it1.525
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.727
r_dihedral_angle_4_deg13.56
r_dihedral_angle_3_deg11.98
r_dihedral_angle_1_deg5.8
r_long_range_B_refined5.639
r_long_range_B_other4.925
r_scangle_other2.486
r_mcangle_other1.859
r_mcangle_it1.857
r_scbond_it1.525
r_scbond_other1.524
r_angle_refined_deg1.408
r_mcbond_it1.108
r_mcbond_other1.095
r_angle_other_deg0.772
r_chiral_restr0.079
r_bond_refined_d0.009
r_gen_planes_refined0.006
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 Atoms2490
Nucleic Acid Atoms
Solvent Atoms401
Heterogen Atoms53

Software

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