4D04

Structure of the Cys65Asp mutant of phenylacetone monooxygenase: reduced state


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.9458.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.879α = 90
b = 107.879β = 90
c = 107.044γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
11.755499.90.089.35.972303
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)
11.761.791000.971.56

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 2YLS1.755468544366899.810.18420.182510.21604RANDOM28.734
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]
0.40.40.4-1.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.145
r_dihedral_angle_4_deg20.402
r_dihedral_angle_3_deg14.845
r_dihedral_angle_1_deg6.157
r_scbond_it3.885
r_mcangle_it3.18
r_mcbond_it2.504
r_mcbond_other2.5
r_angle_refined_deg2.113
r_angle_other_deg0.989
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.145
r_dihedral_angle_4_deg20.402
r_dihedral_angle_3_deg14.845
r_dihedral_angle_1_deg6.157
r_scbond_it3.885
r_mcangle_it3.18
r_mcbond_it2.504
r_mcbond_other2.5
r_angle_refined_deg2.113
r_angle_other_deg0.989
r_chiral_restr0.142
r_bond_refined_d0.022
r_gen_planes_refined0.011
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 Atoms4235
Nucleic Acid Atoms
Solvent Atoms310
Heterogen Atoms121

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing