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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 2C0U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 24-26% PEG 3350, 30% glycerol, 0.1M Na Cacodylate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 3 58.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.934 α = 90 b = 108.934 β = 90 c = 337.671 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 2007-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 NSLS X29A
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 2.4 50 88.2 0.081 22.3 4.1 81048
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) 2.4 2.49 53.7 0.414 1.27 2.2 4878
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 MOLECULAR REPLACEMENT THROUGHOUT 2c0u 2.4 50 76997 4051 88.09 0.20657 0.20364 0.1989 0.2633 0.2528 RANDOM 44.049
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.337 r_dihedral_angle_4_deg 21.334 r_dihedral_angle_3_deg 19.1 r_dihedral_angle_1_deg 7.097 r_scangle_it 3.871 r_scbond_it 2.518 r_angle_refined_deg 2.025 r_mcangle_it 1.565 r_mcbond_it 1.007 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.337 r_dihedral_angle_4_deg 21.334 r_dihedral_angle_3_deg 19.1 r_dihedral_angle_1_deg 7.097 r_scangle_it 3.871 r_scbond_it 2.518 r_angle_refined_deg 2.025 r_mcangle_it 1.565 r_mcbond_it 1.007 r_nbtor_refined 0.308 r_nbd_refined 0.226 r_symmetry_vdw_refined 0.207 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.137 r_bond_refined_d 0.021 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13204 Nucleic Acid Atoms Solvent Atoms 56 Heterogen Atoms 212
Software Software Software Name Purpose REFMAC refinement CBASS data collection HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing