9HVR | pdb_00009hvr

Native glucuronoyl esterase OtCE15A from Opitutus terrae

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GS0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer system 1, pH 6.5 (Imidazole; MES monohydrate (acid)), 37.50 % v/v, Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350).OtCE15A mixed 3:1 with reservoir containing 0.10 M Carboxylic acids (0.2M Sodium formate; 0.2M Ammonium acetate; 0.2M Sodium citrate tribasic dihydrate; 0.2M Potassium sodium tartrate tetrahydrate; 0.2M Sodium oxamate), 0.1 M Buffer system 1, pH 6.5 (Imidazole; MES monohydrate (acid)), 37.50 % v/v, Precipitant Mix 4 (25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350). Glycerol used as cryoprotectant.

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.382	α = 90
b = 64.491	β = 90
c = 117.121	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	100	PIXEL	DECTRIS EIGER X 9M		2022-09-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.88560	ESRF	ID30B

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	1.39	58.561	91.1	0.081	0.082	0.027	0.998	14	8.2		63897

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	1.39	1.43	43.9		0.643	0.778	0.428	0.577	1.6	2.8

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	1.392	58.561	63897	3111	82.764	0.155	0.154	0.1538	0.1697	0.1697	15.369

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			0.035		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.221
r_dihedral_angle_3_deg	12.357
r_dihedral_angle_1_deg	6.586
r_dihedral_angle_2_deg	5.868
r_lrange_it	4.61
r_lrange_other	4.592
r_scangle_it	3.837
r_scangle_other	3.826
r_scbond_it	2.615
r_scbond_other	2.494
r_mcangle_it	2.197
r_mcangle_other	2.196
r_angle_refined_deg	1.915
r_mcbond_it	1.495
r_mcbond_other	1.492
r_angle_other_deg	0.67
r_nbd_refined	0.226
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.189
r_nbd_other	0.182
r_symmetry_nbd_refined	0.159
r_symmetry_xyhbond_nbd_refined	0.104
r_chiral_restr	0.099
r_xyhbond_nbd_refined	0.098
r_metal_ion_refined	0.087
r_symmetry_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3045
Nucleic Acid Atoms
Solvent Atoms	238
Heterogen Atoms	17

Software

Software
Software Name	Purpose
autoPROC	data processing
XDS	data reduction
STARANISO	data scaling
MOLREP	phasing
REFMAC	refinement