7R5C | pdb_00007r5c

Structure of E.coli Class 2 L-asparaginase EcAIII, mutant RDM1-29 (G206C, R207S, D210L, 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, SITTING DROP	7	293	0.1 M PCTP buffer pH 7.0, 25 % w/v PEG 1500

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.789	α = 90
b = 77.864	β = 90
c = 148.363	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		2022-01-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54178

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	2.2	21.48	97.6	0.124	0.14	0.992	6.4	4.5		30380

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	2.2	2.27	99.2		0.496	0.555	0.902	1.9

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	2.2	21.48	30354	1039	97.015	0.251	0.2494	0.25	0.3009	0.3	37.081

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]
0.425			2.441		-2.866

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.657
r_dihedral_angle_4_deg	18.578
r_dihedral_angle_3_deg	16.717
r_dihedral_angle_1_deg	7.52
r_lrange_it	4.961
r_lrange_other	4.956
r_scangle_it	3.432
r_scangle_other	3.432
r_mcangle_other	3.183
r_mcangle_it	3.182
r_scbond_it	2.277
r_scbond_other	2.277
r_mcbond_it	2.134
r_mcbond_other	2.132
r_angle_refined_deg	1.622
r_angle_other_deg	1.385
r_symmetry_xyhbond_nbd_refined	0.25
r_nbd_refined	0.197
r_nbd_other	0.196
r_xyhbond_nbd_refined	0.19
r_symmetry_nbd_other	0.188
r_metal_ion_refined	0.168
r_nbtor_refined	0.157
r_ncsr_local_group_1	0.104
r_symmetry_nbd_refined	0.091
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_2	0.071
r_chiral_restr	0.069
r_symmetry_xyhbond_nbd_other	0.063
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.006
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4193
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	14

Software

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