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Assimilatory nitrite reductase (Nii3) - N226K mutant - SO3 full complex from tobacco leaf
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 277 PEG4000, Tris-HCl, MgCl2, MPD, Na2SO3, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.61 52.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.889 α = 90 b = 132.889 β = 90 c = 77.646 γ = 90
Symmetry Space Group P 4 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210r Rh coated collimating and focusing Si mirror 2010-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 2.07 50 99.9 0.098 7.6 12.6 42057 42057 33.4
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 2.07 2.18 100 0.396 6.48 11.5 4138
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3B0G 2.07 29.2 42014 42014 2120 100 0.2256 0.2226 0.2243 0.2822 0.2815 RANDOM 28.7045
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] 0.39 0.39 -0.79
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_3_deg 16.119 r_dihedral_angle_4_deg 13.112 r_dihedral_angle_1_deg 6.567 r_scangle_it 2.966 r_scbond_it 1.855 r_angle_refined_deg 1.497 r_mcangle_it 1.117 r_mcbond_it 0.624 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.58 r_dihedral_angle_3_deg 16.119 r_dihedral_angle_4_deg 13.112 r_dihedral_angle_1_deg 6.567 r_scangle_it 2.966 r_scbond_it 1.855 r_angle_refined_deg 1.497 r_mcangle_it 1.117 r_mcbond_it 0.624 r_nbtor_refined 0.305 r_metal_ion_refined 0.288 r_symmetry_hbond_refined 0.282 r_xyhbond_nbd_refined 0.224 r_nbd_refined 0.22 r_symmetry_vdw_refined 0.189 r_chiral_restr 0.097 r_bond_refined_d 0.013 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 721 Heterogen Atoms 78
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction