7R1G | pdb_00007r1g

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-38 (R207C, D210S, S211V)

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	8.5	293	30% PEG 4000, 0.2 M MgCl2 in 0.1M Tris-HCl pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.815	α = 90
b = 74.691	β = 90
c = 147.358	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		2020-05-28	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	1.95	21.131	95.3	0.099	0.121	0.991	7	2.7		38942

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	1.95	2			0.361	0.464	0.741	2.1

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	1.95	21.131	38826	1020	94.765	0.249	0.248	0.25	0.2832	0.29	15.092

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]
2.384			-1.841		-0.543

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.595
r_dihedral_angle_4_deg	15.245
r_dihedral_angle_3_deg	14.753
r_dihedral_angle_1_deg	7.528
r_lrange_it	3.479
r_lrange_other	3.451
r_angle_refined_deg	1.617
r_angle_other_deg	1.38
r_mcangle_other	1.024
r_mcangle_it	1.023
r_scangle_it	1.015
r_scangle_other	1.015
r_scbond_it	0.619
r_scbond_other	0.618
r_mcbond_it	0.576
r_mcbond_other	0.575
r_nbd_other	0.303
r_symmetry_nbd_refined	0.268
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_refined	0.217
r_symmetry_nbd_other	0.187
r_metal_ion_refined	0.178
r_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.16
r_symmetry_nbtor_other	0.084
r_chiral_restr	0.07
r_symmetry_xyhbond_nbd_other	0.043
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_gen_planes_other	0.004
r_bond_other_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4180
Nucleic Acid Atoms
Solvent Atoms	170
Heterogen Atoms	2

Software

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