8WGQ | pdb_00008wgq

The Crystal Structure of L-asparaginase from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5I4B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M NaAc, 0.1M Na3citrate pH5.5, 10% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.83

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.223	α = 90
b = 133.223	β = 90
c = 166.786	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	DECTRIS PILATUS 6M		2021-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18064	CLSI	08B1-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.75	47.44	100	0.161	10.2	9.4		45056

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.75	2.85			0.95

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.75	47.44	45011	2241	99.936	0.174	0.1705	0.18	0.2362	0.24	60.416

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]
-1.138	-0.569		-1.138		3.691

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.82
r_dihedral_angle_6_deg	13.499
r_lrange_other	7.044
r_lrange_it	7.043
r_dihedral_angle_1_deg	6.874
r_scangle_it	4.991
r_scangle_other	4.991
r_mcangle_it	4.898
r_mcangle_other	4.898
r_dihedral_angle_2_deg	4.757
r_mcbond_it	3.241
r_mcbond_other	3.241
r_scbond_it	3.233
r_scbond_other	3.233
r_angle_refined_deg	1.028
r_angle_other_deg	0.343
r_nbd_refined	0.207
r_symmetry_nbd_other	0.183
r_nbd_other	0.176
r_nbtor_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.147
r_symmetry_nbd_refined	0.099
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.045
r_bond_refined_d	0.004
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9550
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	32

Software

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