9HVN | pdb_00009hvn

Atomic resolution crystal structure of the hexameric antimicrobial peptide Magainin-2

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	35% MPD, 20 mM HEPES, pH 7

Crystal Properties
Matthews coefficient	Solvent content
1.92	36.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.359	α = 90
b = 34.359	β = 90
c = 55.795	γ = 120

Symmetry
Space Group	P 63 2 2

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		2017-12-07	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.05	29.76	97.81	0.029	0.99	27.36	8.1		9455

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.077			0.92	0.51		4.35

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	1.05	29.756	9455	946	97.807	0.168	0.1674	0.1766	0.177	0.1886	22.402

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]
-0.035	-0.017		-0.035		0.113

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.358
r_dihedral_angle_6_deg	10.873
r_rigid_bond_restr	5.667
r_lrange_it	5.02
r_lrange_other	5.002
r_scangle_it	3.189
r_scangle_other	3.178
r_mcangle_it	2.5
r_dihedral_angle_1_deg	2.448
r_scbond_it	2.329
r_scbond_other	2.32
r_mcangle_other	2.172
r_mcbond_it	1.756
r_mcbond_other	1.755
r_angle_refined_deg	1.553
r_angle_other_deg	0.515
r_nbd_other	0.322
r_symmetry_nbd_refined	0.29
r_symmetry_xyhbond_nbd_refined	0.287
r_nbd_refined	0.243
r_nbtor_refined	0.21
r_symmetry_nbd_other	0.169
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.065
r_xyhbond_nbd_refined	0.022
r_bond_refined_d	0.014
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	168
Nucleic Acid Atoms
Solvent Atoms	10
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BUCCANEER	phasing