9TW9 | pdb_00009tw9

Legionella monocytogenes SodA wt

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2RCV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.2 M Ammonium chloride, 0.1 M Sodium acetate pH 5.0, 20% w/v PEG 6000

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.72	α = 90
b = 94.09	β = 90
c = 94.52	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		2021-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89842	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	52.72	99.7	0.971	7	11.4		57150

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68			0.541		10.5

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	MOLECULAR REPLACEMENT	FREE R-VALUE	1.65	47.26	57060	2869	99.571	0.217	0.2148	0.2148	0.2586	0.2588	24.456

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]
0.657			-0.281		-0.375

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.322
r_dihedral_angle_3_deg	15.401
r_dihedral_angle_6_deg	14.039
r_dihedral_angle_1_deg	12.36
r_lrange_it	6.388
r_lrange_other	6.388
r_scangle_it	5.758
r_scangle_other	5.756
r_scbond_it	4.195
r_scbond_other	4.194
r_mcangle_it	3.487
r_mcangle_other	3.487
r_mcbond_it	2.811
r_mcbond_other	2.811
r_angle_refined_deg	2.011
r_angle_other_deg	0.889
r_chiral_restr_other	0.395
r_symmetry_xyhbond_nbd_refined	0.379
r_symmetry_nbd_refined	0.323
r_nbd_refined	0.248
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.189
r_nbd_other	0.179
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.115
r_symmetry_nbtor_other	0.086
r_ncsr_local_group_1	0.082
r_metal_ion_refined	0.058
r_bond_refined_d	0.014
r_gen_planes_refined	0.014
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3190
Nucleic Acid Atoms
Solvent Atoms	398
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
PHASER	phasing
Coot	model building
BUCCANEER	model building