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assimilatory nitrite reductase (Nii3) - N226K mutant - HCO3 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, NaHCO3, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.65 53.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.616 α = 90 b = 133.616 β = 90 c = 77.742 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 1.5 50 98.8 0.093 6.9 11.8 110538 110538 20.4
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 1.5 1.55 97.1 0.45 3.83 10.7 10692
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 1.5 35.94 110392 110392 5519 100 0.1637 0.1629 0.1606 0.1788 0.1757 RANDOM 15.0942
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] -0.14 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.993 r_dihedral_angle_4_deg 12.859 r_dihedral_angle_3_deg 11.786 r_dihedral_angle_1_deg 5.979 r_scangle_it 2.838 r_scbond_it 1.724 r_angle_refined_deg 1.254 r_mcangle_it 0.987 r_mcbond_it 0.511 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.993 r_dihedral_angle_4_deg 12.859 r_dihedral_angle_3_deg 11.786 r_dihedral_angle_1_deg 5.979 r_scangle_it 2.838 r_scbond_it 1.724 r_angle_refined_deg 1.254 r_mcangle_it 0.987 r_mcbond_it 0.511 r_nbtor_refined 0.305 r_nbd_refined 0.205 r_metal_ion_refined 0.195 r_symmetry_hbond_refined 0.166 r_symmetry_vdw_refined 0.138 r_xyhbond_nbd_refined 0.127 r_chiral_restr 0.084 r_bond_refined_d 0.008 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 924 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