6GS3 | pdb_00006gs3

Crystal Structure of the Uperin-3.5 peptide from Uperoleia mjobergii forming cross-alpha fibril

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Reservoir contained 0.1 M KSCN, 0.1 M MES 6.03 pH, 20 %v/v Jeff 600 with cryo-protection of 20% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
1.53	19.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 19.7	α = 90
b = 28.44	β = 106.95
c = 20.32	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 R 4M		2017-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-3	0.9677	ESRF	MASSIF-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	1.45	19.44	97	0.085	0.089	0.999	15.7	10.636		3777			21.604

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.49	94.7		0.601	0.648	0.908	2.72	7.568

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	AB INITIO PHASING	THROUGHOUT	1.45	19.44	3398	378	97.24	0.189	0.185	0.19	0.2288	0.23	RANDOM	14.461

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]
-0.29		-0.03	-1.1		1.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.735
r_dihedral_angle_3_deg	15.579
r_dihedral_angle_4_deg	6.228
r_dihedral_angle_1_deg	4.162
r_angle_refined_deg	1.783
r_angle_other_deg	0.946
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.735
r_dihedral_angle_3_deg	15.579
r_dihedral_angle_4_deg	6.228
r_dihedral_angle_1_deg	4.162
r_angle_refined_deg	1.783
r_angle_other_deg	0.946
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	250
Nucleic Acid Atoms
Solvent Atoms	16
Heterogen Atoms	5

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Arcimboldo	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.