6UGC | pdb_00006ugc

C3 symmetric peptide design number 3

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	0.1 M Cadmium chloride, 0.1 M Sodium acetate pH 4.6, 30% PEG 400

Crystal Properties
Matthews coefficient	Solvent content
1.53	19.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.03	α = 90
b = 51.03	β = 90
c = 36.02	γ = 120

Symmetry
Space Group	P 3 1 c

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		2019-04-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.77490	APS	24-ID-C

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	0.9	25.51	78.7	0.086	0.112	0.989	5.85	2.242		30646			7.496

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	0.9	0.92	66.4		0.464	0.572	0.854	2.16	2.388

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	0.9	25.51	27581	3065	78.73	0.1205	0.118	0.12	0.1429	0.15	RANDOM	7.195

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]
-0.08	-0.04		-0.08		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.175
r_dihedral_angle_3_deg	12.935
r_dihedral_angle_1_deg	5.572
r_rigid_bond_restr	3.625
r_angle_refined_deg	2.116
r_angle_other_deg	0.823
r_chiral_restr	0.141
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.175
r_dihedral_angle_3_deg	12.935
r_dihedral_angle_1_deg	5.572
r_rigid_bond_restr	3.625
r_angle_refined_deg	2.116
r_angle_other_deg	0.823
r_chiral_restr	0.141
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_gen_planes_other	0.005
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	621
Nucleic Acid Atoms
Solvent Atoms	110
Heterogen Atoms	31

Software

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