8BI3

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200W (crystal M200W#1)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	20-30% PEG4000, 10-15% PEG400, 0.2 M CaCl2 in 100 mM Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.692	α = 90
b = 70.844	β = 90
c = 149.581	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)	0.97630	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	1.45	74.79	99.6	0.085	0.088	0.999	16.1	13		117826

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	1.45	1.48			1.828	1.907	0.797	1.6	12.4

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	2ZAL	1.452	74.79	117709	1068	99.644	0.127	0.1268	0.1621	24.445

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]
1.023			1.528		-2.551

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.392
r_dihedral_angle_4_deg	14.896
r_dihedral_angle_3_deg	11.744
r_dihedral_angle_1_deg	6.273
r_lrange_it	4.879
r_lrange_other	4.54
r_scangle_it	4.206
r_scangle_other	4.205
r_scbond_it	3.493
r_scbond_other	3.493
r_mcangle_other	2.774
r_mcangle_it	2.765
r_rigid_bond_restr	2.253
r_mcbond_it	2.181
r_mcbond_other	2.165
r_angle_other_deg	1.509
r_angle_refined_deg	1.495
r_symmetry_nbd_refined	0.262
r_nbd_other	0.222
r_nbd_refined	0.216
r_symmetry_xyhbond_nbd_refined	0.177
r_symmetry_metal_ion_refined	0.171
r_symmetry_nbd_other	0.17
r_nbtor_refined	0.159
r_xyhbond_nbd_refined	0.148
r_metal_ion_refined	0.114
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4267
Nucleic Acid Atoms
Solvent Atoms	656
Heterogen Atoms	56

Software

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