8COL

Crystal structure of Rhizobium etli constitutive L-asparaginase ReAIV (orthorombic form R4oP-2)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M Tris pH 8.5, 0.2 M MgCl2, 17.5% PEG 8000, 0.3% dodecyl-beta-D-maltoside (DDM)

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.101	α = 90
b = 89.749	β = 90
c = 169.197	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 16M		2022-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9763	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	84.6	99.7	0.135	0.148	0.998	10.22	5.94		86068			34.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.12			1.115	1.22	0.681	1.45	6.11

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	84.599	86052	1000	99.711	0.177	0.1767	0.2343	31.057

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]
-2.121			4.47		-2.349

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.233
r_dihedral_angle_other_3_deg	23.673
r_dihedral_angle_4_deg	15.999
r_dihedral_angle_3_deg	13.74
r_dihedral_angle_1_deg	6.991
r_lrange_it	4.909
r_lrange_other	4.907
r_scangle_it	3.333
r_scangle_other	3.332
r_mcangle_it	2.415
r_mcangle_other	2.415
r_scbond_it	2.152
r_scbond_other	2.152
r_angle_refined_deg	1.731
r_mcbond_it	1.674
r_mcbond_other	1.674
r_angle_other_deg	1.48
r_symmetry_xyhbond_nbd_refined	0.212
r_nbd_refined	0.209
r_symmetry_nbd_refined	0.197
r_symmetry_nbd_other	0.189
r_xyhbond_nbd_refined	0.185
r_nbd_other	0.173
r_nbtor_refined	0.162
r_xyhbond_nbd_other	0.103
r_metal_ion_refined	0.102
r_symmetry_metal_ion_refined	0.094
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.078
r_symmetry_xyhbond_nbd_other	0.041
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9878
Nucleic Acid Atoms
Solvent Atoms	882
Heterogen Atoms	31

Software

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