6FFS

Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease inhibitors

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2XYA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	2.0 M Ammonium Sulfate 0.1 M Na Acetate, pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.657	α = 90
b = 77.657	β = 90
c = 87.855	γ = 120

Symmetry
Space Group	P 32 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 2M		2014-03-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.99988	SLS	X10SA

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	1.86	87.86	100	0.104	0.11	0.035	0.999	21.9	9.8		26331

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	1.86	2.08	100		0.389	0.411	0.131	0.966		9.8

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	2xya	1.86	20	24961	1309	99.84	0.1496	0.1484	0.1719	RANDOM	20.381

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]
0.37	0.19		0.37		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.309
r_dihedral_angle_4_deg	22.475
r_dihedral_angle_3_deg	11.471
r_dihedral_angle_1_deg	6.908
r_angle_refined_deg	1.693
r_angle_other_deg	1.031
r_chiral_restr	0.115
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.309
r_dihedral_angle_4_deg	22.475
r_dihedral_angle_3_deg	11.471
r_dihedral_angle_1_deg	6.908
r_angle_refined_deg	1.693
r_angle_other_deg	1.031
r_chiral_restr	0.115
r_gen_planes_refined	0.023
r_gen_planes_other	0.019
r_bond_refined_d	0.014
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1415
Nucleic Acid Atoms
Solvent Atoms	222
Heterogen Atoms	81

Software

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