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Nitrosomonas europaea Rh50 and mechanism of conduction by Rhesus protein family of channels
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NS1 PDB entry 2NS1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 1:1 microliter drop ratio of (Protein in 0.02M HEPES pH 7.4, 0.1M NaCl, 0.04M B-octyl glucoside, 2mM Dithiothreitol) and (100mM HEPES, 25% PEG 400). Cryoprotected with 10% Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.91 57.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.675 α = 90 b = 96.675 β = 90 c = 137.621 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 78 CCD ADSC QUANTUM 4 2007-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.99 50 99.8 0.097 14.7 6.3 32561 2 23.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.99 2.07 98.2 0.395 2.4 3.1 3221
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2NS1 1.99 40.06 1 32561 30705 1646 98.9 0.19831 0.1963 0.19628 0.2047 0.23666 0.2435 RANDOM 27.769
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] 1.92 0.96 1.92 -2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_3_deg 12.961 r_dihedral_angle_4_deg 11.362 r_dihedral_angle_1_deg 5.689 r_mcangle_it 3.736 r_scangle_it 3.554 r_mcbond_it 3.192 r_scbond_it 2.681 r_angle_refined_deg 1.487 r_mcbond_other 0.986
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.356 r_dihedral_angle_3_deg 12.961 r_dihedral_angle_4_deg 11.362 r_dihedral_angle_1_deg 5.689 r_mcangle_it 3.736 r_scangle_it 3.554 r_mcbond_it 3.192 r_scbond_it 2.681 r_angle_refined_deg 1.487 r_mcbond_other 0.986 r_angle_other_deg 0.929 r_nbd_refined 0.245 r_symmetry_vdw_other 0.238 r_nbtor_refined 0.198 r_nbd_other 0.179 r_xyhbond_nbd_refined 0.167 r_symmetry_hbond_refined 0.151 r_chiral_restr 0.096 r_symmetry_vdw_refined 0.091 r_nbtor_other 0.088 r_xyhbond_nbd_other 0.068 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2806 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data reduction HKL-2000 data scaling PHASER phasing