6T2D

Multicomponent Peptide Stapling as a Diversity-Driven Tool for the Development of Inhibitors of Protein-Protein Interactions

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RV1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.1M TRIS pH 8, 0.2M Ammonium Sulfate, 30% PEG-3350

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.017	α = 90
b = 41.017	β = 90
c = 104.995	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	100	PIXEL	DECTRIS PILATUS 6M-F	double crystal monochromator	2018-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, DESY BEAMLINE P11	1.0332	PETRA III, DESY	P11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.65	35.52	99.7	0.068	0.073	0.024	0.999	18.1	8.9		12894

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.68	95.3		0.803	0.86	0.302	0.899		7.4

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1rv1	1.8	35.52	9597	451	99.96	0.1364	0.1323	0.2257	RANDOM	20.772

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]
-0.1	-0.05		-0.1		0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.524
r_sphericity_free	30.52
r_sphericity_bonded	20.755
r_dihedral_angle_3_deg	14.932
r_dihedral_angle_4_deg	14.776
r_dihedral_angle_1_deg	6.154
r_rigid_bond_restr	3.162
r_angle_refined_deg	1.993
r_angle_other_deg	0.957
r_chiral_restr	0.095

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.524
r_sphericity_free	30.52
r_sphericity_bonded	20.755
r_dihedral_angle_3_deg	14.932
r_dihedral_angle_4_deg	14.776
r_dihedral_angle_1_deg	6.154
r_rigid_bond_restr	3.162
r_angle_refined_deg	1.993
r_angle_other_deg	0.957
r_chiral_restr	0.095
r_bond_refined_d	0.025
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	823
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	39

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	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.