4D03

Structure of the Cys65Asp mutant of phenylacetone monooxygenase: oxidised state


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2YLSPDB ENTRY 2YLS

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.9248

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.739α = 90
b = 107.739β = 90
c = 106.804γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PIXELMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.8541000.0613.97.565099
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)
11.81.8599.90.752.47.5

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2YLS1.8193.361615332199.780.194930.193060.23021RANDOM35.862
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]
0.720.360.72-2.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.412
r_dihedral_angle_4_deg20.095
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.226
r_scbond_it3.968
r_mcangle_it3.733
r_mcbond_it3.073
r_mcbond_other3.069
r_angle_refined_deg2.006
r_angle_other_deg0.926
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.412
r_dihedral_angle_4_deg20.095
r_dihedral_angle_3_deg15.113
r_dihedral_angle_1_deg6.226
r_scbond_it3.968
r_mcangle_it3.733
r_mcbond_it3.073
r_mcbond_other3.069
r_angle_refined_deg2.006
r_angle_other_deg0.926
r_chiral_restr0.124
r_bond_refined_d0.019
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4239
Nucleic Acid Atoms
Solvent Atoms208
Heterogen Atoms131

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing