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Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with low X-ray dose
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 2.59 52.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.107 α = 90 b = 133.107 β = 90 c = 77.796 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 270 Vertical and horizontal Silicon single crystal mirrors 2008-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
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 1.4 50 97.4 0.118 0.118 6.4 6.5 134915 134915 21.7
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 1.4 1.45 77.2 0.404 2.52 6 10563
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 (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 3B0G 1.4 29.25 134844 134844 6773 100 0.1757 0.1757 0.175 0.1711 0.1892 0.1856 RANDOM 16.8876
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] -0.31 -0.31 0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_dihedral_angle_4_deg 13.163 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.471 r_scbond_it 1.51 r_angle_refined_deg 1.217 r_mcangle_it 0.886 r_mcbond_it 0.455 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_dihedral_angle_4_deg 13.163 r_dihedral_angle_3_deg 11.86 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.471 r_scbond_it 1.51 r_angle_refined_deg 1.217 r_mcangle_it 0.886 r_mcbond_it 0.455 r_nbtor_refined 0.306 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.144 r_symmetry_hbond_refined 0.118 r_metal_ion_refined 0.101 r_xyhbond_nbd_refined 0.096 r_chiral_restr 0.082 r_bond_refined_d 0.007 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4246 Nucleic Acid Atoms Solvent Atoms 922 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