9DAH | pdb_00009dah

L-asparaginase II (EcA2-4M)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NNS

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
2.13	42.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.083	α = 90
b = 133.902	β = 109.461
c = 63.123	γ = 90

Symmetry
Space Group	C 1 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 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	2.7	44.48	99.79	0.804	16.302	20		15937

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	2.7	2.8			0.804

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	2.7	44.48	15937	797	99.787	0.243	0.2408	0.2442	0.2751	0.2751	34.652

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]
0.049		0.051	-0.062		-0.018

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.003
r_dihedral_angle_6_deg	14.948
r_dihedral_angle_2_deg	8.493
r_dihedral_angle_1_deg	7.851
r_lrange_it	7.707
r_lrange_other	7.703
r_scangle_it	5.36
r_scangle_other	5.359
r_mcangle_it	5.273
r_mcangle_other	5.273
r_scbond_it	3.431
r_scbond_other	3.43
r_mcbond_it	3.368
r_mcbond_other	3.367
r_angle_refined_deg	1.896
r_angle_other_deg	0.641
r_nbd_refined	0.231
r_symmetry_nbd_other	0.214
r_nbd_other	0.199
r_symmetry_xyhbond_nbd_refined	0.194
r_xyhbond_nbd_refined	0.185
r_nbtor_refined	0.182
r_symmetry_nbd_refined	0.174
r_symmetry_xyhbond_nbd_other	0.111
r_chiral_restr	0.086
r_symmetry_nbtor_other	0.086
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4862
Nucleic Acid Atoms
Solvent Atoms	65
Heterogen Atoms	18

Software

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