8AGN | pdb_00008agn

Cyclohexane epoxide low pH soak of epoxide hydrolase from metagenomic source ch65

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7.5	291	Morpheus crystallisation kit condition H8, 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350 . The crystal was soaked for 2 hours in cryoprotectant containing 1mM of cyclohexane oxide at pH 4.5.

Crystal Properties
Matthews coefficient	Solvent content
2.31	46.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.851	α = 90
b = 47.33	β = 91.707
c = 142.611	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		2018-10-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

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	1.957	142.548	99.7	0.999	10	3.4		102758

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	1.957	1.991	99.7		0.303		3.4

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	1.957	142.548	92853	4502	99.681	0.208	0.2055	0.21	0.2587	0.26	54.15

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]
-3.405		-0.919	5.268		-1.805

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.967
r_dihedral_angle_4_deg	21.336
r_dihedral_angle_3_deg	17.455
r_lrange_it	13.402
r_scangle_it	12.855
r_scbond_it	10.857
r_mcangle_it	10.434
r_mcbond_it	8.851
r_dihedral_angle_1_deg	6.608
r_angle_refined_deg	1.64
r_nbtor_refined	0.304
r_symmetry_nbd_refined	0.222
r_nbd_refined	0.214
r_xyhbond_nbd_refined	0.139
r_symmetry_xyhbond_nbd_refined	0.106
r_chiral_restr	0.104
r_ncsr_local_group_1	0.082
r_ncsr_local_group_3	0.081
r_ncsr_local_group_2	0.08
r_ncsr_local_group_5	0.078
r_ncsr_local_group_4	0.076
r_ncsr_local_group_6	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9543
Nucleic Acid Atoms
Solvent Atoms	272
Heterogen Atoms	135

Software

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