4RG4 | pdb_00004rg4

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4RG3	PDB entry 4RG3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	277	40% 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 coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.145	α = 90
b = 67.028	β = 90
c = 133.576	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	RIGAKU SATURN 944+	VariMax HF	2012-03-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.5418

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	66.79	94.4	0.064	0.064	11.1	3.7	16633	16633			50.03

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)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	77.5		0.5	0.5		1.7	673

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 4RG3	2.51	66.79	16591	16591	1678	94.09	0.1908	0.1908	0.1825	0.19	0.2641	0.27	RANDOM	39.2568

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			-1.39		2.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	17.769
r_dihedral_angle_3_deg	16.455
r_dihedral_angle_1_deg	6.833
r_mcangle_it	4.206
r_mcbond_it	2.752
r_mcbond_other	2.75
r_angle_refined_deg	1.795
r_angle_other_deg	0.909
r_chiral_restr	0.088

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.159
r_dihedral_angle_4_deg	17.769
r_dihedral_angle_3_deg	16.455
r_dihedral_angle_1_deg	6.833
r_mcangle_it	4.206
r_mcbond_it	2.752
r_mcbond_other	2.75
r_angle_refined_deg	1.795
r_angle_other_deg	0.909
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3872
Nucleic Acid Atoms
Solvent Atoms	53
Heterogen Atoms	119

Software

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