7O76 | pdb_00007o76

Reversible supramolecular assembly of the anti-microbial peptide plectasin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3E7U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		300	15 mg/mL plectasin in 10 mM His pH 4.5 added to a reservoir of 0.1 M NH4Ac, 0.1 M Tris pH 8.5 and 40% isopropanol

Crystal Properties
Matthews coefficient	Solvent content
1.7	27.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 23.678	α = 90
b = 20.093	β = 104.279
c = 32.546	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	DECTRIS EIGER X 16M	Kirkpatrick-Baez (KB) mirror pair (VFM, HFM)	2020-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX IV BEAMLINE BioMAX	0.97247	MAX IV	BioMAX

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	1.13	31.53	89.9	0.999	22.49	6		10216

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	1.13	1.2			0.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	3E7U	1.131	21.219	10215	507	90.231	0.147	0.1457	0.15	0.1781	0.18	27.922

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]
2.945		1.224	-2.283		-1.137

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.955
r_dihedral_angle_3_deg	22.952
r_lrange_it	7.751
r_scangle_it	7.73
r_scangle_other	7.495
r_scbond_it	7.27
r_scbond_other	7.005
r_lrange_other	6.994
r_rigid_bond_restr	6.438
r_dihedral_angle_1_deg	4.441
r_mcangle_it	3.414
r_mcangle_other	3.406
r_mcbond_other	2.671
r_mcbond_it	2.667
r_angle_refined_deg	1.965
r_angle_other_deg	0.686
r_symmetry_nbd_refined	0.261
r_nbd_other	0.255
r_nbd_refined	0.252
r_symmetry_nbd_other	0.244
r_nbtor_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.177
r_xyhbond_nbd_refined	0.153
r_symmetry_nbtor_other	0.098
r_chiral_restr	0.095
r_bond_refined_d	0.018
r_gen_planes_refined	0.014
r_bond_other_d	0.004
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	305
Nucleic Acid Atoms
Solvent Atoms	24
Heterogen Atoms	7

Software

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