9GRB | pdb_00009grb

Crystal structure of mouse Carboxylesterase 2b (Ces2b)

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	7.4	293.15	H2 Morpheus II screen (40 mM polyamines (0.1 M spermine tetrahydrochloride, 0.1 M spermidine trihydrochloride, 0.1 M 1,4-diaminobutane dihydrochloride, 0.1 M DL-ornithine monohydrochloride), 0.1 M buffer system 4 at pH 6.5 (1 M MOPSO, Bis-Tris), and 32.5% v/v precipitant mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-hexanetriol))

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.75	α = 90
b = 109.801	β = 92.886
c = 135.435	γ = 90

Symmetry
Space Group	C 1 2 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 EIGER2 X 16M		2021-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.033190	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	2.55	46.91	99.26	0.08605	0.09302	0.03497	0.998	15.26	7		85640			60.07

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.641	99.93		0.7941	0.8556	0.316	0.862	2.66	7.3

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	2.55	46.905	85632	4466	99.277	0.173	0.1709	0.171	0.2049	0.2051	69.146

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]
-0.066		0.021	0.052		0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.881
r_dihedral_angle_3_deg	14.098
r_lrange_it	11.378
r_scangle_it	8.285
r_dihedral_angle_2_deg	7.086
r_dihedral_angle_1_deg	6.616
r_mcangle_it	6.08
r_scbond_it	5.818
r_mcbond_it	4.016
r_angle_refined_deg	1.805
r_nbtor_refined	0.305
r_symmetry_nbd_refined	0.288
r_nbd_refined	0.215
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.125
r_ncsr_local_group_1	0.098
r_ncsr_local_group_5	0.097
r_ncsr_local_group_2	0.096
r_ncsr_local_group_6	0.094
r_ncsr_local_group_3	0.087
r_ncsr_local_group_4	0.08
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16234
Nucleic Acid Atoms
Solvent Atoms	571
Heterogen Atoms	62

Software

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