☰ Navigation Tabs
Assimilatory nitrite reductase (Nii3) - NO2 complex from tobbaco leaf analysed with high 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 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 134.165 α = 90 b = 134.165 β = 90 c = 78.002 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 315r Two dimensional focusing mirror 2011-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 0.9 SPring-8 BL38B1
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 1.6 50 99.5 0.079 0.079 7.8 13.2 93509 93509 20.5
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 1.6 1.66 97.8 0.425 5.9 12.8 9068
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 1.6 37.22 93327 93327 4679 100 0.1531 0.1531 0.1524 0.1512 0.1647 0.1629 RANDOM 15.4695
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] 0.05 0.05 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 13.576 r_dihedral_angle_3_deg 11.78 r_dihedral_angle_1_deg 6.057 r_scangle_it 2.952 r_scbond_it 1.785 r_angle_refined_deg 1.254 r_mcangle_it 0.989 r_mcbond_it 0.504 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.937 r_dihedral_angle_4_deg 13.576 r_dihedral_angle_3_deg 11.78 r_dihedral_angle_1_deg 6.057 r_scangle_it 2.952 r_scbond_it 1.785 r_angle_refined_deg 1.254 r_mcangle_it 0.989 r_mcbond_it 0.504 r_nbtor_refined 0.306 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.147 r_metal_ion_refined 0.128 r_xyhbond_nbd_refined 0.114 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4246 Nucleic Acid Atoms Solvent Atoms 1020 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