9G73 | pdb_00009g73

Crystal structure of mouse Carboxylesterase 2e (Ces2e)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8AXC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	Protein stock solution in 20 mM Tris/HCl, pH 7.4, and 150 mM NaCl; ShotGun (SG1) Screen: E1 (2.0 M ammonium sulfate and 0.1 M Bis-Tris buffer pH 5.5) with protein end concentration of 2.89 mg/ml in a 0.5 uL drop

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 126.931	α = 90
b = 145.243	β = 90
c = 149.432	γ = 90

Symmetry
Space Group	C 2 2 21

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 EIGER2 X 9M		2022-01-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873128	ESRF	ID23-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	80.646	99.9	0.0755	0.994	9.38	2		54113

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.486			0.4157	0.723	2.19

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.4	80.646	54111	2718	99.856	0.178	0.1756	0.1772	0.2138	0.2146	36.312

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]
-1.461			-1.111		2.572

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.213
r_dihedral_angle_4_deg	19.211
r_dihedral_angle_3_deg	13.344
r_lrange_it	10.309
r_lrange_other	10.228
r_dihedral_angle_1_deg	7.041
r_scangle_other	6.504
r_scangle_it	6.499
r_mcangle_it	4.875
r_mcangle_other	4.875
r_scbond_it	4.134
r_scbond_other	4.13
r_mcbond_it	3.018
r_mcbond_other	3.007
r_angle_refined_deg	1.543
r_angle_other_deg	1.301
r_ext_dist_refined_d	0.281
r_nbd_other	0.22
r_nbd_refined	0.194
r_symmetry_nbd_refined	0.189
r_xyhbond_nbd_refined	0.178
r_symmetry_nbd_other	0.171
r_nbtor_refined	0.16
r_symmetry_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.094
r_symmetry_nbtor_other	0.091
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8154
Nucleic Acid Atoms
Solvent Atoms	698
Heterogen Atoms	249

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing