7QYX

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-24 (R207A, D210S, S211T)

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
2.06	40.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.258	α = 90
b = 74.141	β = 90
c = 147.466	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	1.85	52.335	98.4	0.119	0.118	0.999	15.16	13.1		48066

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	1.85	1.95	97.7		2.141	1.852	0.789	1.75	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	1.85	52.335	47941	1031	99.948	0.199	0.1984	0.2385	32.827

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]
4.174			0.061		-4.235

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.211
r_dihedral_angle_4_deg	14.485
r_dihedral_angle_3_deg	13.892
r_dihedral_angle_1_deg	6.889
r_lrange_it	5.559
r_lrange_other	5.542
r_scangle_it	3.808
r_scangle_other	3.806
r_mcangle_other	2.633
r_mcangle_it	2.631
r_scbond_it	2.439
r_scbond_other	2.434
r_mcbond_it	1.779
r_mcbond_other	1.767
r_angle_refined_deg	1.568
r_angle_other_deg	1.484
r_nbd_other	0.236
r_symmetry_xyhbond_nbd_refined	0.218
r_nbd_refined	0.208
r_symmetry_nbd_refined	0.196
r_symmetry_nbd_other	0.178
r_nbtor_refined	0.163
r_xyhbond_nbd_refined	0.147
r_metal_ion_refined	0.104
r_symmetry_nbtor_other	0.088
r_chiral_restr	0.075
r_ncsr_local_group_1	0.062
r_ncsr_local_group_2	0.051
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4063
Nucleic Acid Atoms
Solvent Atoms	208
Heterogen Atoms	5

Software

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