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Assimilatory nitrite reductase (Nii3) - N226K mutant - NO2 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, NaNO2, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.229 α = 90 b = 133.229 β = 90 c = 77.644 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 2010-02-24 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 1.695 50 98.4 0.063 11.6 12 76165 76165 26.4
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 1.695 1.76 94.7 0.506 5.24 11.1 7216
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 1.695 26.76 75977 75977 3819 100 0.1642 0.163 0.1621 0.1857 0.1848 RANDOM 21.0945
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] 0.38 0.38 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.479 r_dihedral_angle_4_deg 12.431 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_1_deg 6.021 r_scangle_it 3.385 r_scbond_it 2.075 r_angle_refined_deg 1.297 r_mcangle_it 1.169 r_mcbond_it 0.617 r_metal_ion_refined 0.373
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.479 r_dihedral_angle_4_deg 12.431 r_dihedral_angle_3_deg 12.277 r_dihedral_angle_1_deg 6.021 r_scangle_it 3.385 r_scbond_it 2.075 r_angle_refined_deg 1.297 r_mcangle_it 1.169 r_mcbond_it 0.617 r_metal_ion_refined 0.373 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.219 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.154 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.089 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 77
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction