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M175E 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 2.65 53.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.551 α = 90 b = 133.551 β = 90 c = 77.805 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 98.4 0.078 0.078 38.28 11.9 76243 76423 23
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 93.7 0.431 7 10.4 7152
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 30.69 76059 72239 3820 100 0.1581 0.1581 0.1571 0.1557 0.1762 0.1747 RANDOM 16.7332
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] -0.14 -0.14 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.623 r_dihedral_angle_4_deg 12.959 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.966 r_scangle_it 3.301 r_scbond_it 1.996 r_angle_refined_deg 1.293 r_mcangle_it 1.129 r_mcbond_it 0.579 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.623 r_dihedral_angle_4_deg 12.959 r_dihedral_angle_3_deg 12.559 r_dihedral_angle_1_deg 5.966 r_scangle_it 3.301 r_scbond_it 1.996 r_angle_refined_deg 1.293 r_mcangle_it 1.129 r_mcbond_it 0.579 r_nbtor_refined 0.304 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.203 r_symmetry_vdw_refined 0.171 r_xyhbond_nbd_refined 0.169 r_metal_ion_refined 0.133 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4248 Nucleic Acid Atoms Solvent Atoms 800 Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing