9DAF | pdb_00009daf

L-asparaginase II (EcA2-K12)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.1	298	0.2 M Ammonium acetate, 20% w/v Polyethylene glycol 3,350.

Crystal Properties
Matthews coefficient	Solvent content
1.98	38.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.746	α = 90
b = 123.051	β = 108.98
c = 79.071	γ = 90

Symmetry
Space Group	P 1 21 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 2M		2023-12-21	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	2.35	47.51	99.93	0.843	14.57	20		44971

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	2.35	47.51			0.843

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	2.35	47.509	44971	2249	99.927	0.177	0.1728	0.1799	0.2494	0.2513	22.873

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]
-0.014		-0.003	0.005		0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.21
r_dihedral_angle_3_deg	15.132
r_dihedral_angle_2_deg	9.768
r_dihedral_angle_1_deg	7.373
r_lrange_it	6.924
r_lrange_other	6.912
r_scangle_it	4.255
r_scangle_other	4.254
r_mcangle_it	3.79
r_mcangle_other	3.79
r_scbond_it	2.583
r_scbond_other	2.583
r_mcbond_it	2.329
r_mcbond_other	2.328
r_angle_refined_deg	1.723
r_angle_other_deg	0.583
r_symmetry_xyhbond_nbd_refined	0.273
r_symmetry_nbd_refined	0.244
r_nbd_refined	0.214
r_symmetry_nbd_other	0.207
r_nbd_other	0.204
r_nbtor_refined	0.174
r_xyhbond_nbd_refined	0.164
r_symmetry_xyhbond_nbd_other	0.114
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.08
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9724
Nucleic Acid Atoms
Solvent Atoms	462
Heterogen Atoms	61

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling