6NDA

RHODOCETIN IN COMPLEX WITH THE INTEGRIN ALPHA2-A DOMAIN AND CADMIUM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5THP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.1 M TRIS, 2.65 M Ammonium SULPHATE

Crystal Properties
Matthews coefficient	Solvent content
3.5	64.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 130.53	α = 90
b = 130.53	β = 90
c = 250.919	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU	mirrors	2010-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU R-AXIS IV	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	3.15	130.53	94	0.107	0.121	0.054	10.9	4.4		67910

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.32	90.2		0.416	0.416	0.472	0.214	1.8	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	5THP	3.15	92.47	64376	3402	93.74	0.2149	0.2119	0.2713	RANDOM	51.751

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]
1.7			1.7		-3.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.934
r_dihedral_angle_4_deg	19.026
r_dihedral_angle_3_deg	18.939
r_dihedral_angle_1_deg	9.709
r_angle_refined_deg	1.462
r_angle_other_deg	1.188
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.934
r_dihedral_angle_4_deg	19.026
r_dihedral_angle_3_deg	18.939
r_dihedral_angle_1_deg	9.709
r_angle_refined_deg	1.462
r_angle_other_deg	1.188
r_chiral_restr	0.05
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21486
Nucleic Acid Atoms
Solvent Atoms	7
Heterogen Atoms	97

Software

Software
Software Name	Purpose
SCALA	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.