8AGS | pdb_00008ags

Cyclohexane epoxide soak of epoxide hydrolase from metagenomic source ch65 resulting in halogenated compound in the active site

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH		291	Morpheus crystallisation kit C1; 40% v/v PEG 500* MME; 20% w/v PEG 20000, thecrystal was soaked with cyclohexane epoxide substrate at pH 6.5 for 2 hours to produce halogenated product.

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.21	α = 90
b = 46.19	β = 98
c = 92.14	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		2018-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97625	Diamond	I03

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	1.61	46.19	97.5	0.999	12.2	3.2		73190

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	1.61	1.64			0.43

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	1.61	45.663	73175	3603	97.448	0.182	0.1803	0.18	0.2226	0.22	33.552

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]
-1.032		-1.534	0.244		1.173

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.828
r_dihedral_angle_4_deg	23.874
r_dihedral_angle_3_deg	16.664
r_lrange_it	11.018
r_scangle_it	10.36
r_scbond_it	8.969
r_mcangle_it	6.892
r_mcbond_it	5.896
r_dihedral_angle_1_deg	5.804
r_angle_refined_deg	1.727
r_nbtor_refined	0.32
r_symmetry_nbd_refined	0.28
r_nbd_refined	0.23
r_symmetry_xyhbond_nbd_refined	0.179
r_xyhbond_nbd_refined	0.174
r_chiral_restr	0.118
r_ncsr_local_group_1	0.116
r_bond_refined_d	0.011
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4839
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	83

Software

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