3EK9 | pdb_00003ek9

SPRY Domain-containing SOCS Box Protein 2: Crystal Structure and Residues Critical for Protein Binding

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FNJ	PDB entry 2FNJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	EVAPORATION	6.5	293	100mM Bis-Tris, pH6.5, 200mM MgCl2, 25% PEG3350, EVAPORATION, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.255	α = 90
b = 68.176	β = 90
c = 69.012	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	IMAGE PLATE	RIGAKU RAXIS IV	AXCO	2007-06-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54

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	2.6	30.7	94	0.117		3.7	5018	5002	2	1

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	2.6	2.69	93.9		0.356	3.2	3.3	493

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 entry 2FNJ	2.6	30.69	4795	223	93.76	0.17277	0.16808	0.17	0.27269	0.27	RANDOM	17.309

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]
-0.1			-1.19		1.29

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.096
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_4_deg	15.681
r_dihedral_angle_1_deg	6.412
r_scangle_it	5.516
r_scbond_it	3.518
r_mcangle_it	2.24
r_angle_refined_deg	1.431
r_mcbond_it	1.219
r_chiral_restr	0.091

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.096
r_dihedral_angle_3_deg	16.038
r_dihedral_angle_4_deg	15.681
r_dihedral_angle_1_deg	6.412
r_scangle_it	5.516
r_scbond_it	3.518
r_mcangle_it	2.24
r_angle_refined_deg	1.431
r_mcbond_it	1.219
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1476
Nucleic Acid Atoms
Solvent Atoms	59
Heterogen Atoms	6

Software

Software
Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

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.