7QTC | pdb_00007qtc

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-3 (G206H, R207T, D210P, S211Q)

X-RAY DIFFRACTION

---

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	8.5	293	20% PEG 6000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.353	α = 90
b = 75.039	β = 90
c = 149.032	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-6000HE		2020-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	Agilent SuperNova	1.54056

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	2.55	20.36	92.7	0.119	0.143	0.983	7.2	2.8		17974

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	2.55	2.66	95.3		0.676	0.83	0.604	2.1	2.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	2ZAL	2.55	20.358	17932	1010	92.044	0.205	0.2023	0.21	0.2483	0.25	33.407

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]
0.204			1.543		-1.747

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.155
r_dihedral_angle_4_deg	17.894
r_dihedral_angle_3_deg	15.067
r_dihedral_angle_1_deg	7.093
r_lrange_it	5.949
r_lrange_other	5.925
r_mcangle_it	2.611
r_mcangle_other	2.61
r_scangle_it	2.374
r_scangle_other	2.373
r_angle_refined_deg	1.585
r_mcbond_it	1.468
r_mcbond_other	1.467
r_angle_other_deg	1.39
r_scbond_it	1.365
r_scbond_other	1.363
r_symmetry_xyhbond_nbd_refined	0.399
r_nbd_other	0.326
r_symmetry_nbd_refined	0.325
r_nbd_refined	0.205
r_symmetry_nbd_other	0.197
r_metal_ion_refined	0.187
r_nbtor_refined	0.157
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.133
r_ncsr_local_group_2	0.126
r_symmetry_nbtor_other	0.08
r_chiral_restr	0.065
r_symmetry_xyhbond_nbd_other	0.044
r_bond_refined_d	0.009
r_bond_other_d	0.007
r_gen_planes_refined	0.006
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4022
Nucleic Acid Atoms
Solvent Atoms	142
Heterogen Atoms	2

Software

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