4RG3

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UCLPDB ENTRY 3UCL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.527760% PEG 3350, 0.1 M bicine, 0.1 M epsilon-caprolactone, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.0239.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.698α = 90
b = 67.06β = 90
c = 131.641γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray93CCDRAYONIX MX-300Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips2011-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949216062006739CLSI08ID-1

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
11.942598.30.1160.1169.913.4364103641027.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.951.9891.412.71687

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 3UCL1.9424.033623536235367097.720.170.170.16460.2179RANDOM30.2361
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]
-0.71-0.451.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg15.254
r_dihedral_angle_3_deg15.112
r_dihedral_angle_1_deg6.624
r_mcangle_it3.201
r_mcbond_it2.326
r_mcbond_other2.324
r_angle_refined_deg1.829
r_angle_other_deg0.911
r_chiral_restr0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.707
r_dihedral_angle_4_deg15.254
r_dihedral_angle_3_deg15.112
r_dihedral_angle_1_deg6.624
r_mcangle_it3.201
r_mcbond_it2.326
r_mcbond_other2.324
r_angle_refined_deg1.829
r_angle_other_deg0.911
r_chiral_restr0.12
r_bond_refined_d0.017
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4060
Nucleic Acid Atoms
Solvent Atoms138
Heterogen Atoms120

Software

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