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The second Ca2+-binding domain of the Na+-Ca2+ exchanger is essential for regulation: crystal structures and mutational analysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QVK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 293 21% (w/v) PEG-3350, 0.1 M HEPES (pH 6.3), CBD2 at 15 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.97 36.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.03 α = 90 b = 59.232 β = 90 c = 22.592 γ = 90
Symmetry Space Group P 21 21 2
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 2007-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 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 1.703 48.8 99.8 0.069 25.4 12.8 12622
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) 1.703 1.76 98.2 0.489 3 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2QVK 1.703 48.8 12622 656 99.67 0.18635 0.18469 0.1834 0.21926 0.221 RANDOM 16.66
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] -0.37 0.86 -0.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 13.454 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 6.528 r_scangle_it 5.345 r_scbond_it 3.178 r_mcangle_it 1.757 r_angle_refined_deg 1.448 r_mcbond_it 1.213 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.449 r_dihedral_angle_4_deg 13.454 r_dihedral_angle_3_deg 12.253 r_dihedral_angle_1_deg 6.528 r_scangle_it 5.345 r_scbond_it 3.178 r_mcangle_it 1.757 r_angle_refined_deg 1.448 r_mcbond_it 1.213 r_nbtor_refined 0.308 r_symmetry_vdw_refined 0.238 r_nbd_refined 0.21 r_symmetry_hbond_refined 0.111 r_chiral_restr 0.108 r_xyhbond_nbd_refined 0.106 r_metal_ion_refined 0.057 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 939 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 2
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling