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Crystal structure of the sodium - potassium pump in the E2.2K+.Pi state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B8E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Dialysis 7 298 pH 7.0, Dialysis, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.08 60.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 223.815 α = 90 b = 50.914 β = 105.12 c = 163.786 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 2 1 CCD RAYONIX MX225HE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
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 2.4 50 99.1 0.058 38.8 17 70710 70074
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 2.4 2.46 95.7 0.372 2.8 5.8 5155
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 THROUGHOUT 3B8E 2.4 15 66157 3555 100 0.24772 0.24644 0.2463 0.27124 0.2746 RANDOM 59.782
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] 2.05 -1.99 0.01 -3.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.775 r_dihedral_angle_4_deg 15.787 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_1_deg 4.084 r_scangle_it 1.467 r_angle_refined_deg 1.085 r_mcangle_it 1.032 r_scbond_it 0.863 r_mcbond_it 0.564 r_chiral_restr 0.068
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.775 r_dihedral_angle_4_deg 15.787 r_dihedral_angle_3_deg 14.955 r_dihedral_angle_1_deg 4.084 r_scangle_it 1.467 r_angle_refined_deg 1.085 r_mcangle_it 1.032 r_scbond_it 0.863 r_mcbond_it 0.564 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 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 Atoms Number Protein Atoms 10131 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CNS phasing