8UOW | pdb_00008uow

Structure of atypical asparaginase from Rhodospirillum rubrum (mutant Y21A)

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2 uL 16 mg/mL protein in 50 mM HEPES, pH 7, 150 mM sodium chloride + 0.2 uL reservoir (Molecular Dimensions Morpheus III F8)

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.831	α = 90
b = 77.119	β = 90
c = 114.845	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 EIGER X 16M		2022-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0	APS	22-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.6	40	98.5	0.051	0.057	0.025	0.991	23.3	4.7		84496

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	97.3		0.326	0.367	0.164	0.948		4.6

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.6	38.8	81672	2582	97.61	0.18738	0.18632	0.2	0.22131	0.23	RANDOM	17.85

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]
			-0.14		0.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	22.437
r_dihedral_angle_3_deg	13.049
r_dihedral_angle_4_deg	11.593
r_dihedral_angle_1_deg	6.672
r_long_range_B_refined	6.232
r_long_range_B_other	6.067
r_scangle_other	4.448
r_scbond_it	2.85
r_scbond_other	2.85
r_mcangle_other	2.83
r_mcangle_it	2.827
r_angle_refined_deg	1.874
r_mcbond_it	1.833
r_mcbond_other	1.825
r_angle_other_deg	1.517
r_chiral_restr	0.085
r_bond_refined_d	0.013
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4723
Nucleic Acid Atoms
Solvent Atoms	616
Heterogen Atoms	32

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data scaling
HKL-2000	data reduction
PHASER	phasing