5DBR

Ca2+ CaM with human cardiac Na+ channel (NaV1.5) inactivation gate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP42980.2M sodium malonate pH 4.0, 20% w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.7154.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.086α = 90
b = 58.086β = 90
c = 102.638γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352013-07-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.2550.399.580.090518.415.69401
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.252.31000.44554.110.56

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 REPLACEMENTTHROUGHOUT4DJC2.2550.3940154399.580.22360.220.2842RANDOM39.957
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]
1.220.611.22-3.95
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg29.8
r_dihedral_angle_2_deg27.785
r_dihedral_angle_3_deg17.83
r_dihedral_angle_1_deg6.42
r_mcangle_it4.434
r_mcbond_it3.35
r_mcbond_other3.338
r_angle_refined_deg1.913
r_angle_other_deg1.101
r_chiral_restr0.105
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_4_deg29.8
r_dihedral_angle_2_deg27.785
r_dihedral_angle_3_deg17.83
r_dihedral_angle_1_deg6.42
r_mcangle_it4.434
r_mcbond_it3.35
r_mcbond_other3.338
r_angle_refined_deg1.913
r_angle_other_deg1.101
r_chiral_restr0.105
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1196
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PROTEUM PLUSdata reduction