☰ Navigation Tabs
M175K 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 2.62 53.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.152 α = 90 b = 133.152 β = 90 c = 77.586 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 1.9 50 99.1 0.089 0.089 11 12.6 55082 55082 27.6
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 1.9 1.97 97.5 0.367 6.63 12 5321
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 1.9 30.59 55017 52226 2791 100 0.1645 0.1645 0.1628 0.1621 0.1967 0.1954 RANDOM 21.8465
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] 0.02 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 13.648 r_dihedral_angle_4_deg 13.556 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.695 r_scbond_it 2.276 r_angle_refined_deg 1.429 r_mcangle_it 1.32 r_mcbond_it 0.719 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.017 r_dihedral_angle_3_deg 13.648 r_dihedral_angle_4_deg 13.556 r_dihedral_angle_1_deg 6.317 r_scangle_it 3.695 r_scbond_it 2.276 r_angle_refined_deg 1.429 r_mcangle_it 1.32 r_mcbond_it 0.719 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.244 r_nbd_refined 0.205 r_symmetry_vdw_refined 0.189 r_xyhbond_nbd_refined 0.183 r_metal_ion_refined 0.141 r_chiral_restr 0.099 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 682 Heterogen Atoms 74
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction MOLREP phasing