5A7G

Comparison of the structure and activity of glycosylated and aglycosylated Human Carboxylesterase 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5A7F	PDB ENTRY 5A7F

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	277	CRYSTALS WERE GROWN AT 4C IN 0.1 M BICINE/TRIZMA BASE, PH 8.5, CONTAINING 0.03 M EACH OF DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 10 % (W/V) PEG 4000, 20 % (V/V) GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.39	α = 90
b = 115.39	β = 90
c = 128.14	γ = 120

Symmetry
Space Group	H 3

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	MIRRORS	2013-10-18	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.48	53.94	98.4	0.05	11.1	2.9		104388

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.48	1.52	91.8		0.69	1	2

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 (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	PDB ENTRY 5A7F	1.48	46.55	93337	4985	92.68	0.13137	0.12916	0.14	0.17277	0.18	RANDOM	31.014

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]
0.16	0.16		0.16		-0.53

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	65.49
r_dihedral_angle_2_deg	32.301
r_sphericity_bonded	24.361
r_dihedral_angle_4_deg	15.897
r_dihedral_angle_3_deg	11.853
r_dihedral_angle_1_deg	8.568
r_long_range_B_refined	6.44
r_long_range_B_other	5.633
r_scangle_other	4.958
r_scbond_other	4.299
r_scbond_it	4.298
r_mcangle_it	4.113
r_mcangle_other	4.113
r_rigid_bond_restr	3.589
r_mcbond_it	3.367
r_mcbond_other	3.365
r_angle_refined_deg	1.51
r_angle_other_deg	0.924
r_chiral_restr	0.093
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4107
Nucleic Acid Atoms
Solvent Atoms	695
Heterogen Atoms	14

Software

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