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Structural Basis for Ca2+ Selectivity of a Voltage-gated Calcium Channel
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3RVY PDB ENTRY 3RVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.75 298 CHAPSO: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 = 177.765 α = 90 b = 177.685 β = 132.64 c = 131.205 γ = 90
Symmetry Space Group C 1 2 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 ADSC QUANTUM 315 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.75 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 3.198 30 93.4 0.076 5 46122 46122 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.198 3.37 100 0.5 2.5 4.9
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 (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 PDB ENTRY 3RVY 3.198 29.89 43749 43749 2335 93.2 0.23802 0.23671 0.2379 0.26254 0.2649 RANDOM 95.553
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 -1.09 3.45 -1.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_long_range_B_refined 19.143 r_long_range_B_other 19.142 r_dihedral_angle_3_deg 18.89 r_dihedral_angle_4_deg 18.138 r_mcangle_other 13.965 r_mcangle_it 13.961 r_scangle_other 12.676 r_mcbond_it 9.223 r_mcbond_other 9.223
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.409 r_long_range_B_refined 19.143 r_long_range_B_other 19.142 r_dihedral_angle_3_deg 18.89 r_dihedral_angle_4_deg 18.138 r_mcangle_other 13.965 r_mcangle_it 13.961 r_scangle_other 12.676 r_mcbond_it 9.223 r_mcbond_other 9.223 r_scbond_other 8.291 r_scbond_it 8.261 r_dihedral_angle_1_deg 5.027 r_angle_refined_deg 1.584 r_angle_other_deg 0.849 r_chiral_restr 0.075 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 7196 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 191
Software Software Software Name Purpose HKL-2000 data collection PHENIX model building REFMAC refinement MOSFLM data reduction SCALA data scaling PHENIX phasing