4I3N

Crystal structure of rabbit ryanodine receptor 1 (residues 1-536) disease mutant D61N


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION9.5pH 9.5, EVAPORATION
Crystal Properties
Matthews coefficientSolvent content
6.9482.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 168.629α = 90
b = 168.629β = 90
c = 301.647γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 325 mm CCD2010-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97949SSRLBL9-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.9548.6810011.43500011
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.11100

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2XOA2.9548.683325017501000.22730.228790.22730.25716RANDOM89.806
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]
0.930.460.93-1.39
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.928
r_dihedral_angle_3_deg17.54
r_dihedral_angle_4_deg15.222
r_dihedral_angle_1_deg5.101
r_angle_refined_deg0.992
r_scangle_it0.868
r_mcangle_it0.516
r_scbond_it0.496
r_mcbond_it0.275
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.928
r_dihedral_angle_3_deg17.54
r_dihedral_angle_4_deg15.222
r_dihedral_angle_1_deg5.101
r_angle_refined_deg0.992
r_scangle_it0.868
r_mcangle_it0.516
r_scbond_it0.496
r_mcbond_it0.275
r_chiral_restr0.064
r_bond_refined_d0.006
r_gen_planes_refined0.003
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_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3546
Nucleic Acid Atoms
Solvent Atoms14
Heterogen Atoms6

Software

Software
Software NamePurpose
Web-Icedata collection
PHASERphasing
REFMACrefinement
SCALAdata scaling