4MVU

Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3RVYPDB ENTRY 3RVY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.75298CHAPSO:DMPC bicelles, 0.1M Na-Acetate, pH4.75, 2M Ammonium Sulfate, 28% Glucose, 15mM Calcium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 177.765α = 90
b = 177.685β = 132.64
c = 131.205γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.11.75ALS8.2.1

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
13.1983093.40.0765461224612211
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)
13.1983.371000.52.54.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 3RVY3.19829.894374943749233593.20.238020.236710.26254RANDOM95.553
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]
2.13-1.093.45-1.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.409
r_long_range_B_refined19.143
r_long_range_B_other19.142
r_dihedral_angle_3_deg18.89
r_dihedral_angle_4_deg18.138
r_mcangle_other13.965
r_mcangle_it13.961
r_scangle_other12.676
r_mcbond_it9.223
r_mcbond_other9.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.409
r_long_range_B_refined19.143
r_long_range_B_other19.142
r_dihedral_angle_3_deg18.89
r_dihedral_angle_4_deg18.138
r_mcangle_other13.965
r_mcangle_it13.961
r_scangle_other12.676
r_mcbond_it9.223
r_mcbond_other9.223
r_scbond_other8.291
r_scbond_it8.261
r_dihedral_angle_1_deg5.027
r_angle_refined_deg1.584
r_angle_other_deg0.849
r_chiral_restr0.075
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7196
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms191

Software

Software
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing