4RG4

Epsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Loose conformation


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4RG3PDB entry 4RG3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP827740% PEG 3350, 0.1 M imidazole, 0.2 M epsilon-caprolactone; crystals were transferred to a fresh drop and cross-linked with glutaraldehyde, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0339.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.145α = 90
b = 67.028β = 90
c = 133.576γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRIGAKU SATURN 944+VariMax HF2012-03-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.566.7994.40.0640.06411.13.7166331663350.03
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5477.50.50.51.7673

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 4RG32.5166.791659116591167894.090.19080.19080.18250.2641RANDOM39.2568
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]
-1.13-1.392.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.159
r_dihedral_angle_4_deg17.769
r_dihedral_angle_3_deg16.455
r_dihedral_angle_1_deg6.833
r_mcangle_it4.206
r_mcbond_it2.752
r_mcbond_other2.75
r_angle_refined_deg1.795
r_angle_other_deg0.909
r_chiral_restr0.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.159
r_dihedral_angle_4_deg17.769
r_dihedral_angle_3_deg16.455
r_dihedral_angle_1_deg6.833
r_mcangle_it4.206
r_mcbond_it2.752
r_mcbond_other2.75
r_angle_refined_deg1.795
r_angle_other_deg0.909
r_chiral_restr0.088
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3872
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms119

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
REFMACphasing