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Mechanistic and Structural Analyses of the Roles of Arg409 and Asp402 in the Reaction of the Flavoprotein Nitroalkane Oxidase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1C0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 25-30%(W/V) PEG 3350, 35% (V/V) GLYCEROL, 200MM SODIUM CACODYLATE TRIHYDRATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.99 58.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.319 α = 90 b = 108.319 β = 90 c = 340.012 γ = 120
Symmetry Space Group P 32 2 1
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 315 mirrors 2006-08-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 0.9795 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.5 50 97.1 0.128 17.1 5.6 81166 81166
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.74 93.2 0.587 1.9 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 THROUGHOUT 1c0u 2.5 50 73886 3776 91.03 0.23 0.228 0.2216 0.277 0.2718 RANDOM 39.771
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] 0.63 0.31 0.63 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.909 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 17.424 r_dihedral_angle_1_deg 5.381 r_scangle_it 2.012 r_angle_refined_deg 1.32 r_scbond_it 1.221 r_mcangle_it 0.802 r_mcbond_it 0.424 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.909 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 17.424 r_dihedral_angle_1_deg 5.381 r_scangle_it 2.012 r_angle_refined_deg 1.32 r_scbond_it 1.221 r_mcangle_it 0.802 r_mcbond_it 0.424 r_nbtor_refined 0.307 r_symmetry_hbond_refined 0.294 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.182 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13228 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing