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Assimilatory nitrite reductase (Nii3) - N226K mutant - ligand free form from tobacco leaf
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B0G PDB ENTRY 3B0G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 8.5 277 PEG4000, Tris-HCl, MgCl2, MPD, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.64 53.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.498 α = 90 b = 133.498 β = 90 c = 77.77 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 1.35 50 100 0.08 8 14.3 152951 152951 18.2
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 1.35 1.4 100 0.468 4.68 13.8 15084
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 PDB ENTRY 3B0G 1.35 47.19 152899 152899 7671 100 0.1649 0.1649 0.1644 0.1612 0.1748 0.1719 RANDOM 14.7481
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] 0.07 0.07 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.259 r_dihedral_angle_4_deg 12.354 r_dihedral_angle_3_deg 11.763 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.507 r_scbond_it 1.536 r_angle_refined_deg 1.227 r_mcangle_it 0.926 r_mcbond_it 0.463 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.259 r_dihedral_angle_4_deg 12.354 r_dihedral_angle_3_deg 11.763 r_dihedral_angle_1_deg 5.982 r_scangle_it 2.507 r_scbond_it 1.536 r_angle_refined_deg 1.227 r_mcangle_it 0.926 r_mcbond_it 0.463 r_nbtor_refined 0.303 r_nbd_refined 0.199 r_metal_ion_refined 0.182 r_symmetry_hbond_refined 0.135 r_symmetry_vdw_refined 0.13 r_xyhbond_nbd_refined 0.101 r_chiral_restr 0.083 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 918 Heterogen Atoms 75
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction