8PX9 | pdb_00008px9

Structure of the antibacterial peptide ABC transporter McjD, solved at wavelength 2.75 A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	10% PEG 4000, 0.1 M ammonium sulphate, 100 mM HEPES pH 7.5 and 22% glycerol

Crystal Properties
Matthews coefficient	Solvent content
3.95	68.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.19	α = 90
b = 109.32	β = 90
c = 233.35	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	80	PIXEL	DECTRIS PILATUS 12M		2017-05-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I23	2.7552	Diamond	I23

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	2.8	54.67	96.8	0.2146	0.2167	0.02965	0.998	12.48	54.6		51873			83.08

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	2.8	2.9			0.675	0.27

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	SAD	THROUGHOUT	2.8	54.67	49306	2578	99.74	0.29406	0.29209	0.3	0.32974	0.33	RANDOM	163.335

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]
4.68			3.23		-7.91

RMS Deviations
Key	Refinement Restraint Deviation
r_long_range_B_refined	18.144
r_long_range_B_other	18.144
r_dihedral_angle_3_deg	15.242
r_scangle_other	12.361
r_mcangle_it	11.399
r_mcangle_other	11.399
r_scbond_it	7.844
r_scbond_other	7.843
r_mcbond_it	7.555
r_mcbond_other	7.555
r_dihedral_angle_2_deg	5.145
r_dihedral_angle_1_deg	3.392
r_angle_refined_deg	1.547
r_angle_other_deg	0.789
r_chiral_restr	0.082
r_bond_refined_d	0.008
r_gen_planes_refined	0.008
r_bond_other_d	0.005
r_gen_planes_other	0.005
r_dihedral_angle_4_deg
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	8913
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	64

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
HKL2Map	phasing