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Crystal Structure of a parallel coiled-coil dimerization domain from the voltage-gated proton channel (oxidation/H2O2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VMX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 283 0.1M KCL, 0.05 M TRIS-HCL PH8.0, 0.1M SODIUM MALONATE, 30% PEG 1000, 5MM H2O2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 283K
Crystal Properties Matthews coefficient Solvent content 1.88 34.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.307 α = 90 b = 54.154 β = 90 c = 81.883 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 90 CCD RAYONIX MX225HE 2010-05-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.55 50 100 0.075 0.075 10.9 12.3 26858 -3
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 1.55 1.58 100 0.48 0.48 4.675 7.4
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 3VMX 1.55 40.94 26774 1346 99.7 0.195 0.193 0.2125 0.233 0.2522 RANDOM 23.77
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] 0.09 0.08 -0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.799 r_dihedral_angle_4_deg 19.931 r_dihedral_angle_3_deg 15.855 r_scangle_it 6.164 r_dihedral_angle_1_deg 4.142 r_scbond_it 3.749 r_mcangle_it 2.404 r_angle_refined_deg 2.36 r_mcbond_it 1.512 r_chiral_restr 0.175
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.799 r_dihedral_angle_4_deg 19.931 r_dihedral_angle_3_deg 15.855 r_scangle_it 6.164 r_dihedral_angle_1_deg 4.142 r_scbond_it 3.749 r_mcangle_it 2.404 r_angle_refined_deg 2.36 r_mcbond_it 1.512 r_chiral_restr 0.175 r_bond_refined_d 0.025 r_gen_planes_refined 0.01 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 1556 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing