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M175G mutant of assimilatory nitrite reductase (Nii3) from tobbaco 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, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.63 53.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.271 α = 90 b = 133.271 β = 90 c = 77.734 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 100 CCD ADSC QUANTUM 210r Rh-coated Si single crystal mirror 2009-10-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0 Photon Factory AR-NW12A
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 1.7 50 96.4 0.061 0.061 13.7 5.4 74661 74661 25.2
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 1.7 1.76 96.2 0.37 4.94 4.5 7340
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 1.7 29.99 74579 70822 3757 100 0.1779 0.1779 0.1765 0.1752 0.2036 0.2021 RANDOM 18.96
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] 0.04 0.04 -0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 13.356 r_dihedral_angle_3_deg 12.403 r_dihedral_angle_1_deg 5.976 r_scangle_it 3.153 r_scbond_it 1.997 r_angle_refined_deg 1.325 r_mcangle_it 1.106 r_mcbond_it 0.6 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.949 r_dihedral_angle_4_deg 13.356 r_dihedral_angle_3_deg 12.403 r_dihedral_angle_1_deg 5.976 r_scangle_it 3.153 r_scbond_it 1.997 r_angle_refined_deg 1.325 r_mcangle_it 1.106 r_mcbond_it 0.6 r_nbtor_refined 0.302 r_nbd_refined 0.205 r_symmetry_hbond_refined 0.205 r_symmetry_vdw_refined 0.159 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.143 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4243 Nucleic Acid Atoms Solvent Atoms 814 Heterogen Atoms 74
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection DENZO data reduction MOLREP phasing