7OS3 | pdb_00007os3

Crystal structure of Rhizobium etli inducible L-asparaginase ReAV solved by S-SAD (orthorhombic form START)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		292	25% PEG3350, 0.2 M Li2SO4, 0.01% (w/v) heptane-1,2,3-triol, 0.1 M Tris pH 8.0

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.15	α = 90
b = 91.05	β = 90
c = 105.84	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	DECTRIS PILATUS 6M		2019-04-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	2.0664	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.177	69.024	98.3	0.088	0.99	21.74	17.8		75182

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.18	2.23	79.4		0.694	0.85	2.07	4.1

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	SAD	FREE R-VALUE	2.177	69.024	39687	1000	98.611	0.169	0.1677	0.18	0.2238	0.23	34.053

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]
-3.307			-2.432		5.738

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.586
r_dihedral_angle_4_deg	22.47
r_dihedral_angle_3_deg	16.661
r_lrange_it	8.391
r_lrange_other	8.344
r_dihedral_angle_1_deg	8.004
r_scangle_it	6.304
r_scangle_other	6.304
r_scbond_it	4.27
r_scbond_other	4.269
r_mcangle_it	3.828
r_mcangle_other	3.825
r_mcbond_it	2.716
r_mcbond_other	2.712
r_angle_refined_deg	1.443
r_angle_other_deg	1.318
r_symmetry_xyhbond_nbd_refined	0.246
r_symmetry_nbd_other	0.213
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.209
r_nbd_other	0.202
r_xyhbond_nbd_refined	0.189
r_nbtor_refined	0.158
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.053
r_chiral_restr	0.052
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5321
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
HKL2Map	phasing