7OU1

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV (monoclinic form MP2)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7OS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	292	2% PEG8000, 20% PEG400, 5 mM Mg(CH3COO)2, 6 mM 3.0 mM sucrose monolaureate

Crystal Properties
Matthews coefficient	Solvent content
2.55	51.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.923	α = 90
b = 91.308	β = 97.111
c = 114.164	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	MARMOSAIC 225 mm CCD		2019-12-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.3	0.8950	BESSY	14.3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.65	45.65	99	0.134	0.995	10	4		189888			21.54

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75	98		0.622	0.795	2.2	4.1

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 (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7OS3	1.65	45.65	189888	1000	99.048	0.19	0.1898	0.2217	16.259

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]
-0.931		0.344	-0.671		1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.435
r_dihedral_angle_4_deg	14.74
r_dihedral_angle_3_deg	13.289
r_dihedral_angle_1_deg	6.404
r_lrange_it	4.596
r_lrange_other	4.545
r_scangle_it	2.636
r_scangle_other	2.636
r_scbond_it	1.702
r_scbond_other	1.702
r_mcangle_it	1.697
r_mcangle_other	1.687
r_angle_refined_deg	1.645
r_angle_other_deg	1.509
r_mcbond_it	1.079
r_mcbond_other	1.068
r_nbd_refined	0.212
r_nbd_other	0.211
r_symmetry_xyhbond_nbd_refined	0.198
r_symmetry_nbd_other	0.184
r_nbtor_refined	0.16
r_symmetry_nbd_refined	0.157
r_xyhbond_nbd_refined	0.156
r_symmetry_xyhbond_nbd_other	0.108
r_chiral_restr	0.091
r_symmetry_nbtor_other	0.082
r_ncsr_local_group_5	0.082
r_ncsr_local_group_6	0.079
r_ncsr_local_group_1	0.077
r_ncsr_local_group_4	0.077
r_ncsr_local_group_2	0.074
r_ncsr_local_group_3	0.058
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10372
Nucleic Acid Atoms
Solvent Atoms	1403
Heterogen Atoms	8

Software

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