6HZX | pdb_00006hzx

Protein-aromatic foldamer complex crystal structure

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KS3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6	293	Ammonium sulfate 0.2M, sodium acetate 0.1M, ph 6.0, PEG 4000 16%, sodium azide 3 mM. HCA 0.3 mM, foldamere 0.3 mM.

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.64	α = 90
b = 82.64	β = 90
c = 106.39	γ = 90

Symmetry
Space Group	P 43

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 9M	Cryogenically cooled channel cut crystal monochromator, convex prefocussing mirror and a Kirkpatrick-Baez pair of focussing mirrors	2018-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 2	0.980112195015	SOLEIL	PROXIMA 2

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	2.91	44.73	99.8	0.093	0.097	0.999	19.95	13.455		15735			60.549

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	2.91	3.09	99.1		0.593	0.618	0.981	3.47	12.707

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	3KS3	2.91	44.73	14907	785	99.54	0.1728	0.1709	0.1814	0.2105	0.2172	RANDOM	80.678

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]
5.51			5.51		-11.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.279
r_dihedral_angle_3_deg	14.496
r_dihedral_angle_4_deg	14.043
r_dihedral_angle_1_deg	7.008
r_angle_other_deg	4.217
r_angle_refined_deg	1.592
r_chiral_restr	0.046
r_bond_other_d	0.034
r_gen_planes_refined	0.03
r_gen_planes_other	0.028

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.279
r_dihedral_angle_3_deg	14.496
r_dihedral_angle_4_deg	14.043
r_dihedral_angle_1_deg	7.008
r_angle_other_deg	4.217
r_angle_refined_deg	1.592
r_chiral_restr	0.046
r_bond_other_d	0.034
r_gen_planes_refined	0.03
r_gen_planes_other	0.028
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3996
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms	666

Software

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

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.