7QYM

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-18 (R207V, D210P, S211W)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	20% PEG 6K; 15% PEG 400; 0.2M MgCl2 in 0.1 Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.552	α = 90
b = 75.006	β = 90
c = 146.95	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 PILATUS 6M		2021-06-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.77490	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	1.2	66.896	98.1	0.085	0.088	0.999	14.2	13.7		167749

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	1.2	1.22	95.7		1.786	1.857	0.556	1.7	13.2

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	1.2	66.896	167684	1086	97.797	0.127	0.127	0.1534	19.234

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]
1.915			1.462		-3.377

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.22
r_dihedral_angle_4_deg	16.675
r_dihedral_angle_3_deg	12.445
r_dihedral_angle_1_deg	6.608
r_lrange_it	4.676
r_lrange_other	4.612
r_scangle_it	4.089
r_scangle_other	4.088
r_scbond_it	3.713
r_scbond_other	3.712
r_rigid_bond_restr	3.304
r_mcangle_other	2.744
r_mcangle_it	2.738
r_mcbond_it	2.183
r_mcbond_other	2.172
r_angle_refined_deg	1.727
r_angle_other_deg	1.605
r_nbd_other	0.296
r_symmetry_nbd_refined	0.289
r_nbd_refined	0.224
r_symmetry_nbd_other	0.182
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.178
r_nbtor_refined	0.172
r_metal_ion_refined	0.11
r_chiral_restr	0.092
r_symmetry_nbtor_other	0.087
r_bond_refined_d	0.013
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4248
Nucleic Acid Atoms
Solvent Atoms	614
Heterogen Atoms	7

Software

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