4FZL | pdb_00004fzl

High resolution structure of truncated bacteriocin syringacin M from Pseudomonas syringae pv. tomato DC3000

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	289	8% w/v PEG 8000, 30% v/v ethylene glycol, 0.13 M CaCl2, 0.03 M MgCl2, 0.1 M Bicine/Tris base, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
3	59.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.81	α = 90
b = 96.09	β = 114.17
c = 64.27	γ = 90

Symmetry
Space Group	P 1 21 1

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	PSI PILATUS 6M	mirrors	2012-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97631	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.46	50.92	99.7	0.052	13.6	6.2	106648	106648			23.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.5	99.7		0.966	2.9	6	7853

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	1.46	50.92	99482	99482	5244	97.88	0.15406	0.15406	0.15157	0.1521	0.20117	0.2	RANDOM	28.937

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]
3.67		1.9	-1.85		-0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	40.403
r_dihedral_angle_2_deg	38.587
r_sphericity_bonded	24.144
r_dihedral_angle_4_deg	15.945
r_dihedral_angle_3_deg	14.792
r_rigid_bond_restr	6.873
r_dihedral_angle_1_deg	6.724
r_angle_refined_deg	2.097
r_angle_other_deg	1.16
r_chiral_restr	0.132
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3645
Nucleic Acid Atoms
Solvent Atoms	551
Heterogen Atoms	57

Software

Software
Software Name	Purpose
EDNA	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling