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Nitroalkane oxidase: active site mutant D402N crystallized with 1-nitrooctane
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2C12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 20-30 mM PEG 3350, 20-35% glycerol, 0.1M NaCacodylate, pH 7.5, vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.96 58.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.996 α = 90 b = 107.996 β = 90 c = 338.576 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 2007-06-11 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 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 2.2 50 93.8 0.06 0.06 11.2 5.5 110228 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.28 64.9 0.434 0.434 1.4 2.4 7485
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2C12 2.2 50 129624 110225 5516 93.87 0.195 0.195 0.193 0.233 0.2172 RANDOM 42.061
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] 0.5 0.25 0.5 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.122 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.851 r_scbond_it 1.85 r_angle_refined_deg 1.353 r_mcangle_it 1.066 r_mcbond_it 0.931 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.122 r_dihedral_angle_4_deg 19.832 r_dihedral_angle_3_deg 15.673 r_dihedral_angle_1_deg 5.321 r_scangle_it 2.851 r_scbond_it 1.85 r_angle_refined_deg 1.353 r_mcangle_it 1.066 r_mcbond_it 0.931 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.258 r_symmetry_vdw_refined 0.236 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.094 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13219 Nucleic Acid Atoms Solvent Atoms 273 Heterogen Atoms 280
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction MOLREP phasing