7R6B | pdb_00007r6b

Crystal structure of mutant R43D/L124D/R125A/C273S of L-Asparaginase I from Yersinia pestis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3NTX

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	0.2 M Calcium acetate, 10% (w/v) PEG 8000, 0.1 M Imidazole/ Hydrochloric acid, pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.263	α = 90
b = 115.893	β = 90
c = 127.548	γ = 90

Symmetry
Space Group	C 2 2 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		2020-03-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim 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	2.03	50	98.7	0.092	0.042	0.997	22	5.7		47794

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.03	2.07	99.5		0.92	0.47	0.719	2.1	4.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3NTX	2.03	48.85	44242	2372	96.16	0.1724	0.1699	0.18	0.2181	0.22	RANDOM	31.099

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]
0.28			0.14		-0.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.174
r_dihedral_angle_4_deg	21.941
r_dihedral_angle_3_deg	14.365
r_dihedral_angle_1_deg	7.989
r_angle_refined_deg	1.993
r_angle_other_deg	1.481
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.174
r_dihedral_angle_4_deg	21.941
r_dihedral_angle_3_deg	14.365
r_dihedral_angle_1_deg	7.989
r_angle_refined_deg	1.993
r_angle_other_deg	1.481
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4646
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	42

Software

Software
Software Name	Purpose
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.