9QBL | pdb_00009qbl

Crystal structure of Xanthobacter autotrophicus SPARDA mutant lacking DREN nuclease domains

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	280	Protein concentration 6.4 mg/ml. Reservoir: Tris-Bicine pH 8.5 0.1 M; Ammonium Tartrate 0.25M; PEG5000 mme 9% (w/v); Glycerol 2% (v/v). Seeding with microcrystals

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.706	α = 90
b = 155.396	β = 90
c = 161.338	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 12M		2019-07-01	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97970,0.97980,0.98000	PETRA III, EMBL c/o DESY	P13 (MX1)

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	1.5	161.34	98.2	0.12	0.127	0.043	0.998	10.3	16.5		284306			28.703

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	1.5	1.53	63.3		1.512	1.86	0.956	0.023	0.6	4

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	MAD	THROUGHOUT	1.5	80.67	240032	27155	92.4	0.2	0.196	0.2028	0.237	0.2384	RANDOM	41.48

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]
0.74			-0.11		-0.63

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.437
r_dihedral_angle_4_deg	19.189
r_dihedral_angle_3_deg	13.874
r_long_range_B_refined	8.75
r_dihedral_angle_1_deg	6.362
r_scbond_it	4.965
r_mcangle_it	4.778
r_mcbond_it	3.505
r_angle_refined_deg	1.545
r_chiral_restr	0.109
r_gen_planes_refined	0.009
r_bond_refined_d	0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11648
Nucleic Acid Atoms
Solvent Atoms	1228
Heterogen Atoms	146

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
Auto-Rickshaw	phasing