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The 1.3 A resolution structure of Nitrosomonas europaea Rh50 and mechanistic implications for NH3 transport by Rhesus family proteins
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NUU PDB Entrty 2NUU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 10mM Tris/HCl pH=8.5, 0.2M NaCl, 24% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3.24 62.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.061 α = 90 b = 100.061 β = 90 c = 143.828 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 100 CCD MARMOSAIC 225 mm CCD 2007-03-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.07209 SLS X06SA
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 1.3 20 99.8 0.06 18.71 131874 -3
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 1.3 1.4 100 0.682
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 (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 Entrty 2NUU 1.3 20 125231 6637 99.83 0.1509 0.14809 0.14692 0.1933 0.17082 0.21 RANDOM 23.28
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] 0.15 0.08 0.15 -0.23
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.435 r_dihedral_angle_3_deg 11.261 r_sphericity_free 10.532 r_dihedral_angle_4_deg 10.411 r_scangle_it 6.147 r_sphericity_bonded 6.045 r_scbond_it 4.712 r_dihedral_angle_1_deg 4.598 r_mcangle_it 3.493 r_mcbond_it 2.848
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.435 r_dihedral_angle_3_deg 11.261 r_sphericity_free 10.532 r_dihedral_angle_4_deg 10.411 r_scangle_it 6.147 r_sphericity_bonded 6.045 r_scbond_it 4.712 r_dihedral_angle_1_deg 4.598 r_mcangle_it 3.493 r_mcbond_it 2.848 r_rigid_bond_restr 2.625 r_angle_refined_deg 1.005 r_nbtor_refined 0.303 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.134 r_xyhbond_nbd_refined 0.084 r_symmetry_hbond_refined 0.081 r_chiral_restr 0.075 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2671 Nucleic Acid Atoms Solvent Atoms 372 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement MAR345 data collection XDS data reduction XSCALE data scaling MOLREP phasing