9JUX | pdb_00009jux

Crystal structure of hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TQH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	COUNTER-DIFFUSION		293.15	0.2M Sodium acetate trihydrate, 0.1M Sodium cacodylate trihydrate pH6.5, 30% w/v Polyethylene glycol 8,000

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.97	α = 90
b = 111.628	β = 90
c = 114.885	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293.15	PIXEL	DECTRIS EIGER X 16M		2023-05-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL44XU	0.9	SPring-8	BL44XU

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	1.667	47.4802	99.58	0.019	0.027	0.019	0.999	16.2	2		88855			26.79

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	1.67	47.48	99.58		0.999

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	1.67	47.48	88429	4453	99.723	0.171	0.1679	0.2121	0.2253	0.2562	20.086

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]
-0.096			-2.162		2.258

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.265
r_dihedral_angle_3_deg	13.025
r_lrange_it	13.013
r_scangle_it	11.261
r_dihedral_angle_2_deg	10.557
r_scbond_it	8.431
r_rigid_bond_restr	7.482
r_mcangle_it	7.436
r_dihedral_angle_1_deg	5.999
r_mcbond_it	5.585
r_angle_refined_deg	2.252
r_nbtor_refined	0.317
r_nbd_refined	0.211
r_symmetry_nbd_refined	0.204
r_symmetry_xyhbond_nbd_refined	0.174
r_chiral_restr	0.144
r_xyhbond_nbd_refined	0.106
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5841
Nucleic Acid Atoms
Solvent Atoms	207
Heterogen Atoms

Software

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