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Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of the Na+-transporting V-ATPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DB4 PDB ENTRY 2DB4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 100mM Tris-HCl pH7.5, 4% Glycerol, 240mM potassium citrate, 35% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 4.82 74.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.41 α = 90 b = 124.937 β = 90 c = 208.221 γ = 90
Symmetry Space Group P 21 21 21
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 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 3.14 48.79 93.8 55386 51929 1 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.14 3.31 94.8 0.671 0.671 1.9 3.7 7587
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2DB4 3.14 48.79 49285 2644 93.8 0.2108 0.20881 0.2104 0.24818 0.2473 RANDOM 71.158
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] -6.88 3.49 3.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.255 r_dihedral_angle_3_deg 18.61 r_dihedral_angle_1_deg 5.018 r_scangle_it 2.114 r_angle_refined_deg 1.391 r_scbond_it 1.198 r_mcangle_it 0.802 r_mcbond_it 0.426 r_chiral_restr 0.103 r_bond_refined_d 0.011
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.255 r_dihedral_angle_3_deg 18.61 r_dihedral_angle_1_deg 5.018 r_scangle_it 2.114 r_angle_refined_deg 1.391 r_scbond_it 1.198 r_mcangle_it 0.802 r_mcbond_it 0.426 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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 11270 Nucleic Acid Atoms Solvent Atoms 6 Heterogen Atoms 228
Software Software Software Name Purpose BSS data collection REFMAC refinement MOSFLM data reduction SCALA data scaling