5CGO | pdb_00005cgo

Structure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 13

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4MGP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	0.1 M Sodium citrate tribasic dihydrate pH 5.6, 35% v/v tert-butanol

Crystal Properties
Matthews coefficient	Solvent content
1.78	30.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 24.85	α = 109.76
b = 27	β = 102.35
c = 29.96	γ = 90.23

Symmetry
Space Group	P 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	CCD	MARMOSAIC 300 mm CCD		2013-10-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.979	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.5	27.45	96.1	0.052	14.94	3.75		10964

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	1.5	1.6	94.4		0.31	5.02	3.75

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 (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	4MGP	1.5	27.45	10395	566	96.1	0.17462	0.17166	0.17	0.23889	0.24	RANDOM	27.15

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]
-2.01	-0.54	0.02	-1.14	1.1	1.67

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	50.239
r_dihedral_angle_2_deg	33.648
r_dihedral_angle_3_deg	14.908
r_dihedral_angle_1_deg	13.184
r_sphericity_bonded	8.825
r_long_range_B_refined	4.253
r_long_range_B_other	3.317
r_scangle_other	2.716
r_scbond_other	2.508
r_scbond_it	2.505
r_mcangle_other	2.379
r_mcangle_it	2.367
r_mcbond_it	1.98
r_mcbond_other	1.952
r_angle_refined_deg	1.773
r_rigid_bond_restr	1.205
r_angle_other_deg	1.025
r_chiral_restr	0.095
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_gen_planes_other	0.004
r_bond_other_d	0.002
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	690
Nucleic Acid Atoms
Solvent Atoms	45
Heterogen Atoms

Software

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