8AGP | pdb_00008agp

Halogenated product of limonene epoxide turnover by epoxide hydrolase from metagenomic source ch65

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	Morpheus crystallisation kit condition C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000. The crystal was incubated with 1mM mixture of cis (1R,2S,4R) and trans (1S,2R,4R) isomers of (+)-limonene oxide for 1 hour 20 mins to produce a halogenated product in the active site.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.12

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.83	α = 90
b = 46.11	β = 98.41
c = 93	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2018-09-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.91587	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	1.49	51.263	99.1	0.998	8.8	3.2		93810

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52			0.366

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5ng7	1.49	51.263	93795	4702	99.067	0.18	0.1779	0.18	0.2156	0.22	26.938

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]
-0.91		-0.937	0.014		1.123

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.286
r_dihedral_angle_4_deg	20.713
r_dihedral_angle_3_deg	14.396
r_lrange_it	9.207
r_scangle_it	8.754
r_scbond_it	7.027
r_dihedral_angle_1_deg	5.999
r_mcangle_it	5.688
r_mcbond_it	4.62
r_angle_refined_deg	1.655
r_nbtor_refined	0.321
r_symmetry_nbd_refined	0.256
r_nbd_refined	0.225
r_symmetry_xyhbond_nbd_refined	0.199
r_xyhbond_nbd_refined	0.156
r_ncsr_local_group_1	0.123
r_chiral_restr	0.116
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4822
Nucleic Acid Atoms
Solvent Atoms	432
Heterogen Atoms	79

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
BUSTER	refinement
PARROT	phasing
Coot	model building