9TWC | pdb_00009twc

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	3LIO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	0.1 M MES/imidazole pH 6.5, 10% w/v PEG 20000, 20% v/v PEG MME 550, 0.02 M of each additive alcohol: 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.19	α = 90
b = 105.58	β = 90
c = 162.58	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		2022-02-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	1	Diamond	I24

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	2	67.48	100	0.997	10	13.1		121479

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	2	2.03			0.443		13.3

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	2	67.472	121391	6036	99.987	0.196	0.194	0.194	0.2273	0.2274	42.896

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]
-1.941			-1.537		3.478

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.289
r_dihedral_angle_3_deg	15.531
r_dihedral_angle_6_deg	15.5
r_lrange_it	8.186
r_lrange_other	8.185
r_scangle_it	6.974
r_scangle_other	6.973
r_dihedral_angle_1_deg	6.24
r_scbond_it	4.767
r_scbond_other	4.767
r_mcangle_it	4.433
r_mcangle_other	4.432
r_mcbond_it	3.426
r_mcbond_other	3.424
r_angle_refined_deg	1.353
r_angle_other_deg	0.482
r_symmetry_nbd_refined	0.273
r_nbd_refined	0.206
r_nbtor_refined	0.191
r_symmetry_nbd_other	0.184
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.134
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.067
r_ncsr_local_group_14	0.058
r_ncsr_local_group_5	0.056
r_ncsr_local_group_15	0.051
r_ncsr_local_group_9	0.05
r_ncsr_local_group_3	0.047
r_ncsr_local_group_7	0.045
r_ncsr_local_group_10	0.045
r_ncsr_local_group_12	0.045
r_ncsr_local_group_2	0.043
r_ncsr_local_group_4	0.041
r_ncsr_local_group_13	0.041
r_ncsr_local_group_1	0.04
r_ncsr_local_group_6	0.038
r_ncsr_local_group_11	0.036
r_ncsr_local_group_8	0.035
r_symmetry_xyhbond_nbd_other	0.01
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9228
Nucleic Acid Atoms
Solvent Atoms	585
Heterogen Atoms	6

Software

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