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Assimilatory nitrite reductase (Nii4) from tobbaco root
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, EDTA, PEG400, pH 8.5, vapor diffusion, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.94 36.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.343 α = 90 b = 112.085 β = 90 c = 92.503 γ = 90
Symmetry Space Group P 21 21 21
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 Bruker DIP-6040 Rh-coated mirror 2008-11-17 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 2.3 50 99.5 0.106 0.106 10.8 2 45883 45735 38.4
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 2.3 2.38 98 0.426 1.9
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 2.306 46.25 45883 43569 2315 100 0.1812 0.178 0.1776 0.2409 0.2386 RANDOM 25.8215
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] 0.81 -2.62 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_3_deg 17.152 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_1_deg 6.861 r_scangle_it 3.175 r_scbond_it 1.964 r_angle_refined_deg 1.553 r_mcangle_it 1.193 r_mcbond_it 0.624 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.92 r_dihedral_angle_3_deg 17.152 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_1_deg 6.861 r_scangle_it 3.175 r_scbond_it 1.964 r_angle_refined_deg 1.553 r_mcangle_it 1.193 r_mcbond_it 0.624 r_nbtor_refined 0.304 r_metal_ion_refined 0.273 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.217 r_symmetry_hbond_refined 0.199 r_xyhbond_nbd_refined 0.167 r_chiral_restr 0.104 r_bond_refined_d 0.014 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8472 Nucleic Acid Atoms Solvent Atoms 497 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing