9BAD | pdb_00009bad

Crystal structure of Bacillus subtilis 168 L-asparaginase II with antileukemic activity

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	285.15	PEG 400 25 %, HEPES 0.1 M, NaCl 0.1 M

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.234	α = 90
b = 104.486	β = 90
c = 123.055	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 2M		2022-12-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS SIRIUS BEAMLINE MANACA	0.97718	LNLS SIRIUS	MANACA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.3	48.135	100	0.99	1.5	1.9		321574

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.32	100		0.54	1.2	2

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 (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	1.3	48.13	305395	16178	99.99	0.13695	0.13552	0.1387	0.16433	0.1666	RANDOM	16.358

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]
0.45			-0.45		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	14.593
r_long_range_B_other	13.409
r_dihedral_angle_3_deg	12.803
r_scangle_other	10.797
r_scbond_it	7.605
r_scbond_other	7.603
r_mcangle_it	6.933
r_mcangle_other	6.932
r_dihedral_angle_2_deg	6.308
r_dihedral_angle_1_deg	6.296
r_mcbond_it	4.902
r_mcbond_other	4.902
r_rigid_bond_restr	4.06
r_angle_refined_deg	1.678
r_angle_other_deg	0.589
r_chiral_restr	0.094
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_dihedral_angle_4_deg
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9427
Nucleic Acid Atoms
Solvent Atoms	1124
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
pointless	data scaling
MOLREP	phasing