8C0I | pdb_00008c0i

Structure of E. coli Class 2 L-asparaginase EcAIII, mutant M200L (acyl-enzyme intermediate)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2ZAL

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20 PEG4000, 10% PEG400, 0.2 M MgCl2 in 100 mM Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.04	39.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.71	α = 90
b = 74.851	β = 90
c = 146.595	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	RIGAKU HyPix-3000		2022-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	RIGAKU PhotonJet-S	1.54184

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.9	19.3	97.6	0.148	0.177	0.949	18	3.1		42775

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.9	97.8		0.283	0.344	0.865	3.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.9	19.3	42735	1022	97.114	0.233	0.2319	0.23	0.2752	0.28	21.496

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]
-1.906			-0.017		1.924

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.11
r_dihedral_angle_4_deg	20.23
r_dihedral_angle_3_deg	14.531
r_dihedral_angle_1_deg	7.492
r_lrange_it	3.221
r_lrange_other	3.14
r_mcangle_it	1.617
r_mcangle_other	1.617
r_angle_refined_deg	1.553
r_scangle_it	1.55
r_scangle_other	1.55
r_angle_other_deg	1.38
r_mcbond_it	0.979
r_mcbond_other	0.978
r_scbond_it	0.938
r_scbond_other	0.937
r_metal_ion_refined	0.221
r_nbd_other	0.216
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_refined	0.201
r_symmetry_nbd_refined	0.196
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.164
r_nbtor_refined	0.159
r_ncsr_local_group_1	0.099
r_ncsr_local_group_2	0.098
r_symmetry_nbtor_other	0.085
r_chiral_restr	0.071
r_symmetry_xyhbond_nbd_other	0.054
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4214
Nucleic Acid Atoms
Solvent Atoms	185
Heterogen Atoms	5

Software

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