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Assimilatory nitrite reductase (Nii3) - N226K mutant - SO3 partial 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 2.65 53.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.657 α = 90 b = 133.657 β = 90 c = 77.823 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 Rh coated collimating and focusing Si mirror 2010-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0 Photon Factory AR-NE3A
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 1.55 50 99.9 0.107 6.3 14.2 101449 101449 22.6
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 1.55 1.61 99.9 0.457 5.15 13.7 9996
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 1.55 35.99 101113 101113 5048 100 0.1644 0.1644 0.1637 0.1612 0.1763 0.1749 RANDOM 16.6108
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] -0.46 -0.46 0.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.011 r_dihedral_angle_4_deg 12.98 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 5.999 r_scangle_it 3.022 r_scbond_it 1.837 r_angle_refined_deg 1.267 r_mcangle_it 1.03 r_mcbond_it 0.525 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.011 r_dihedral_angle_4_deg 12.98 r_dihedral_angle_3_deg 12.032 r_dihedral_angle_1_deg 5.999 r_scangle_it 3.022 r_scbond_it 1.837 r_angle_refined_deg 1.267 r_mcangle_it 1.03 r_mcbond_it 0.525 r_nbtor_refined 0.304 r_metal_ion_refined 0.233 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.179 r_symmetry_vdw_refined 0.139 r_xyhbond_nbd_refined 0.128 r_chiral_restr 0.085 r_bond_refined_d 0.009 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 922 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