3ILA | pdb_00003ila

Crystal structure of rabbit ryanodine receptor 1 N-terminal domain (9-205)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Ryanodine Receptor isoform 2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	295	15-25% PEG 3350, 0.2M sodium chloride, 0.1M BisTris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.15	42.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.734	α = 90
b = 155.705	β = 110.63
c = 81.613	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD	Double Crystal Monochromator, mirrors	2008-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.97949	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.8	50	69.8	0.14	13.28	7.2	36063	32354			59.146

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	45.1		0.416	2.33	3.2	1837

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	Ryanodine Receptor isoform 2	2.9	48.51	34226	28582	1736	93.12	0.27653	0.27653	0.27413	0.27	0.31991	0.32	RANDOM	67.983

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]
6.53		-0.08	-3.67		-2.91

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.317
r_dihedral_angle_3_deg	14.061
r_dihedral_angle_4_deg	11.011
r_dihedral_angle_1_deg	3.982
r_angle_refined_deg	0.784
r_nbtor_refined	0.278
r_scangle_it	0.263
r_mcangle_it	0.225
r_scbond_it	0.165
r_nbd_refined	0.132

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.317
r_dihedral_angle_3_deg	14.061
r_dihedral_angle_4_deg	11.011
r_dihedral_angle_1_deg	3.982
r_angle_refined_deg	0.784
r_nbtor_refined	0.278
r_scangle_it	0.263
r_mcangle_it	0.225
r_scbond_it	0.165
r_nbd_refined	0.132
r_mcbond_it	0.124
r_xyhbond_nbd_refined	0.105
r_symmetry_vdw_refined	0.095
r_symmetry_hbond_refined	0.091
r_chiral_restr	0.046
r_bond_refined_d	0.005
r_gen_planes_refined	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9944
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	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.