4RG3 | pdb_00004rg3

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3UCL	PDB ENTRY 3UCL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	60% PEG 3350, 0.1 M bicine, 0.1 M epsilon-caprolactone, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.15

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	CCD	RAYONIX MX-300	Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips	2011-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949216062006739	CLSI	08ID-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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.94	25	98.3	0.116	0.116	9.9	13.4	36410	36410			27.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	1.98	91.4			12.7	1687

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3UCL	1.94	24.03	36235	36235	3670	97.72	0.17	0.17	0.1646	0.17	0.2179	0.22	RANDOM	30.2361

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			-0.45		1.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.707
r_dihedral_angle_4_deg	15.254
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_1_deg	6.624
r_mcangle_it	3.201
r_mcbond_it	2.326
r_mcbond_other	2.324
r_angle_refined_deg	1.829
r_angle_other_deg	0.911
r_chiral_restr	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.707
r_dihedral_angle_4_deg	15.254
r_dihedral_angle_3_deg	15.112
r_dihedral_angle_1_deg	6.624
r_mcangle_it	3.201
r_mcbond_it	2.326
r_mcbond_other	2.324
r_angle_refined_deg	1.829
r_angle_other_deg	0.911
r_chiral_restr	0.12
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4060
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	120

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.