5V2O

De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	0.1 M MES, pH 6.5, 2.0 M ((NH4)2SO4 , 5 %w/v PEG 400,Protein: 10mg/mL

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.77	α = 89.79
b = 55.34	β = 108.15
c = 58.04	γ = 109.52

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	PIXEL	DECTRIS PILATUS3 S 6M		2016-08-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.82648	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.2	54.81	92.4	0.99	7.8	3		127440

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	1.2	54.8	114886	6236	95.04	0.14583	0.14401	0.144	0.17848	0.1785	RANDOM	20.247

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]
-0.03	0.21	0.19	-0.18	0.4	-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.804
r_sphericity_free	30.451
r_dihedral_angle_4_deg	23.285
r_sphericity_bonded	21.118
r_dihedral_angle_3_deg	12.93
r_long_range_B_refined	9.471
r_mcangle_it	9.208
r_rigid_bond_restr	8.842
r_mcbond_it	7.371
r_scbond_it	6.093
r_dihedral_angle_1_deg	5.8
r_angle_refined_deg	2.901
r_chiral_restr	0.202
r_bond_refined_d	0.032
r_gen_planes_refined	0.014
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2574
Nucleic Acid Atoms
Solvent Atoms	357
Heterogen Atoms	201

Software

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