5M0Z

Cyclohexanone Monooxygenase from T. municipale: reduced enzyme bound to NADP+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5M10 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5293.15100 mM Tris-HCl, 25 % PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.5752.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.206α = 90
b = 114.677β = 90
c = 155.435γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray273.15CCDRAYONIX MX-2252016-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.96863ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.633.78940.0640.99612.231.97654310.11
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.66970.4340.6641.811.9

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 REPLACEMENTTHROUGHOUT5M101.633.7876541234093.770.148770.147850.17736RANDOM12.569
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]
0.660.1-0.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg16.832
r_dihedral_angle_3_deg12.323
r_long_range_B_refined6.63
r_dihedral_angle_1_deg6.524
r_long_range_B_other5.92
r_scangle_other3.543
r_scbond_it2.321
r_scbond_other2.321
r_angle_refined_deg1.986
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.113
r_dihedral_angle_4_deg16.832
r_dihedral_angle_3_deg12.323
r_long_range_B_refined6.63
r_dihedral_angle_1_deg6.524
r_long_range_B_other5.92
r_scangle_other3.543
r_scbond_it2.321
r_scbond_other2.321
r_angle_refined_deg1.986
r_mcangle_other1.54
r_mcangle_it1.539
r_angle_other_deg1.113
r_mcbond_it1.035
r_mcbond_other1.011
r_chiral_restr0.127
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_bond_other_d0.003
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 Atoms4154
Nucleic Acid Atoms
Solvent Atoms807
Heterogen Atoms104

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing