3EMW | pdb_00003emw

Crystal Structure of human splA/ryanodine receptor domain and SOCS box containing 2 (SPSB2) in complex with a 20-residue VASA peptide

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2JK9	PDB ENTRY 2JK9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.178M Na/KPO4, 17.8% PEG3350, 8.88% EtGly, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 34.47	α = 90
b = 61.963	β = 90
c = 118.581	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	ADSC QUANTUM 315		2008-09-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.975653	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	42.83	99.9	0.078	0.078	15	6.9		24366			25.22

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	100		0.618	0.618	3.1	7.1	3494

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 2JK9	1.8	42.83	23115	23073	1239	99.82	0.17995	0.17995	0.17796	0.18	0.21593	0.22	RANDOM	18.523

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]
-1.27			0.97		0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.32
r_dihedral_angle_4_deg	14.46
r_dihedral_angle_3_deg	11.816
r_scangle_it	8.465
r_scbond_it	6.89
r_dihedral_angle_1_deg	6.419
r_mcangle_it	4.479
r_mcbond_it	3.348
r_angle_refined_deg	1.548
r_mcbond_other	1.174

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.32
r_dihedral_angle_4_deg	14.46
r_dihedral_angle_3_deg	11.816
r_scangle_it	8.465
r_scbond_it	6.89
r_dihedral_angle_1_deg	6.419
r_mcangle_it	4.479
r_mcbond_it	3.348
r_angle_refined_deg	1.548
r_mcbond_other	1.174
r_angle_other_deg	0.953
r_chiral_restr	0.092
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1579
Nucleic Acid Atoms
Solvent Atoms	138
Heterogen Atoms	16

Software

Software
Software Name	Purpose
GDA	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	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.