4NNY

Crystal structure of non-phosphorylated form of PKD2 phosphopeptide bound to HLA-A2

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	15% PEG3350, 0.1 M HEPES, 0.2 M sodium chloride, 0.003 M magnesium chloride, 0.003 M cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3	59.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.4	α = 90
b = 79.8	β = 90
c = 110.7	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	100	CCD	RIGAKU SATURN 944		2009-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5417

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	1.9	19.95	99	0.092	16.57	8.2		42471		-3	23.945

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	94.6		0.529	2.92

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	PDB ENTRY 3BH9	1.9	19.95	42471	2133	99.12	0.208	0.207	0.2285	RANDOM	17.3851

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]
-0.2			0.04		0.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.612
r_dihedral_angle_4_deg	18.997
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	5.205
r_scangle_it	2.915
r_scbond_it	1.715
r_mcangle_it	1.147
r_angle_refined_deg	1.072
r_mcbond_it	0.619
r_chiral_restr	0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.612
r_dihedral_angle_4_deg	18.997
r_dihedral_angle_3_deg	12.631
r_dihedral_angle_1_deg	5.205
r_scangle_it	2.915
r_scbond_it	1.715
r_mcangle_it	1.147
r_angle_refined_deg	1.072
r_mcbond_it	0.619
r_chiral_restr	0.077
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3133
Nucleic Acid Atoms
Solvent Atoms	301
Heterogen Atoms	15

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.