8RC7

The structure of membrane-active antibiotic cyclodecapeptide gramicidin S in complex with urea

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				Urea, HCl, 95% Ethanol

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.93

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 25.8	α = 90
b = 25.8	β = 90
c = 21.49	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	293	DIFFRACTOMETER	CUSTOM-MADE		1978-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE		1.5406

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	0.98	22.34	81.1	210			4028

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO PHASING	FREE R-VALUE	0.98	22.34	4028	205	80.738	0.14	0.14	0.1318	Random selection	8.88

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]
0.064	0.032		0.064		-0.208

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	23.292
r_dihedral_angle_3_deg	9.574
r_dihedral_angle_1_deg	7.751
r_lrange_other	4.54
r_lrange_it	4.488
r_scangle_other	4.228
r_scangle_it	4.176
r_scbond_other	2.927
r_scbond_it	2.916
r_angle_refined_deg	2.196
r_chiral_restr	1.735
r_mcangle_it	1.336
r_mcangle_other	1.332
r_mcbond_it	1.023
r_mcbond_other	1.02
r_angle_other_deg	0.881
r_nbd_refined	0.244
r_nbtor_refined	0.221
r_symmetry_nbd_other	0.204
r_symmetry_nbtor_other	0.168
r_xyhbond_nbd_refined	0.119
r_symmetry_xyhbond_nbd_refined	0.118
r_nbd_other	0.114
r_bond_refined_d	0.021
r_gen_planes_refined	0.013
r_bond_other_d	0.004
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	82
Nucleic Acid Atoms
Solvent Atoms	9
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement