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Assimilatory nitrite reductase (Nii3) - NO complex 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, NaNO2, ascorbic acid, pH 8.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.57 52.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.758 α = 90 b = 132.758 β = 90 c = 77.539 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 Bruker DIP-6040 Horizontal focusing mirror 2008-04-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 1.4 50 99.6 0.062 0.062 9 9.1 134875 134875 21.9
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 1.4 1.45 100 0.499 3.58 8.7 13352
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 1.4 23.49 134823 134823 6771 100 0.1617 0.1617 0.1613 0.1595 0.1678 0.166 RANDOM 18.0772
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] -0.1 -0.1 0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.781 r_dihedral_angle_4_deg 12.715 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.688 r_scbond_it 1.636 r_angle_refined_deg 1.214 r_mcangle_it 0.945 r_mcbond_it 0.477 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.781 r_dihedral_angle_4_deg 12.715 r_dihedral_angle_3_deg 11.801 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.688 r_scbond_it 1.636 r_angle_refined_deg 1.214 r_mcangle_it 0.945 r_mcbond_it 0.477 r_nbtor_refined 0.305 r_nbd_refined 0.202 r_symmetry_vdw_refined 0.148 r_symmetry_hbond_refined 0.141 r_metal_ion_refined 0.12 r_xyhbond_nbd_refined 0.1 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 4246 Nucleic Acid Atoms Solvent Atoms 782 Heterogen Atoms 76
Software Software Software Name Purpose SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction