8QVF | pdb_00008qvf

Comparison of room-temperature and cryogenic structures of soluble Epoxide Hydrolase with ligands bound.

X-RAY DIFFRACTION

Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		In-house model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	BATCH MODE		293	32% PEG 3350, 0.1M Li2SO4 and 0.1M Tris-HCl (pH 8.2)

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.41	α = 90
b = 95.41	β = 90
c = 244.29	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	PIXEL	DECTRIS EIGER X 16M		2021-03-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.98	MAX IV	BioMAX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1	silicon nitride membrane (Silson)	fixed target

Fixed Target
Diffraction ID	Description	Sample Holding	Support Base	Motion control	Details	Sample Solvent
1	silicon nitride membrane

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	2.4	44.44	99.94	0.9707	4.49	15.442		63304

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	2.4	2.42			0.3141

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2.4	44.44	26621	1338	100	0.1877	0.1858	0.18	0.2228	0.22	RANDOM	59.85

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]
-5.7565			-5.7565		11.5131

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	17.91
t_omega_torsion	3.08
t_angle_deg	0.94
t_bond_d	0.007
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4309
Nucleic Acid Atoms
Solvent Atoms	98
Heterogen Atoms	24

Software

Software
Software Name	Purpose
BUSTER	refinement
CrystFEL	data reduction
CrystFEL	data scaling
PHASER	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.