6CDX | pdb_00006cdx

High-resolution crystal structure of fluoropropylated cystine knot, binding to alpha-5 beta-6 integrin

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2N8C	PDB entries 2N8C & 2N8B
experimental model	PDB	2N8B	PDB entries 2N8C & 2N8B

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION		298	Isopropanol

Crystal Properties
Matthews coefficient	Solvent content
1.59	22.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 16.95	α = 90
b = 44.25	β = 90
c = 66.41	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	CMOS	RDI CMOS_8M		2016-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 4.2.2	1.000	ALS	4.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	36.82	94.1	0.036	32.3	29		27921

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1

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	PDB entries 2N8C & 2N8B	1	36.82	25665	1341	96.72	0.204	0.2029	0.2	0.2257	0.22	RANDOM	10.152

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]
			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	24.686
r_dihedral_angle_2_deg	18.835
r_dihedral_angle_3_deg	11.798
r_dihedral_angle_1_deg	11.462
r_angle_refined_deg	3.366
r_angle_other_deg	1.703
r_chiral_restr	0.531
r_bond_refined_d	0.032
r_gen_planes_refined	0.016
r_bond_other_d	0.008

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_4_deg	24.686
r_dihedral_angle_2_deg	18.835
r_dihedral_angle_3_deg	11.798
r_dihedral_angle_1_deg	11.462
r_angle_refined_deg	3.366
r_angle_other_deg	1.703
r_chiral_restr	0.531
r_bond_refined_d	0.032
r_gen_planes_refined	0.016
r_bond_other_d	0.008
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	529
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms

Software

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