4JKQ

Crystal structure of the N-terminal region of the human ryanodine receptor 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XOAPDB entry 2XOA

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829520 mM TRIS-HCl, 150 mM NaCl, 10% glycerol, 7mM mercaptoethanol, 1 mM CHAPS, 0.1% betaine, 100 mM HEPES, 200 mM ammonium formate, 21% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.5952.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.45α = 90
b = 75.45β = 90
c = 248.84γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-10-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918BESSY14.1

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.39124.421000.160.1512.213.82946921
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.392.5295

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2XOA2.3944.7727960144499.350.22580.224050.26087RANDOM62.542
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]
1.841.84-3.68
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free74.934
r_dihedral_angle_2_deg37.941
r_sphericity_bonded26.956
r_dihedral_angle_3_deg15.959
r_dihedral_angle_4_deg15.943
r_dihedral_angle_1_deg5.908
r_rigid_bond_restr3.886
r_angle_refined_deg1.185
r_chiral_restr0.082
r_bond_refined_d0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free74.934
r_dihedral_angle_2_deg37.941
r_sphericity_bonded26.956
r_dihedral_angle_3_deg15.959
r_dihedral_angle_4_deg15.943
r_dihedral_angle_1_deg5.908
r_rigid_bond_restr3.886
r_angle_refined_deg1.185
r_chiral_restr0.082
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3934
Nucleic Acid Atoms
Solvent Atoms79
Heterogen Atoms

Software

Software
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling