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Tyr258Phe mutant of NikD, an unusual amino acid oxidase essential for nikkomycin biosynthesis: open form at 1.55A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OLO PDB entry 2OLO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.6 298 4 mL of the Tyr258Phe mutant protein (at 10 mg/mL) was mixed with 4 mL 20-30% 2-methyl-2,4-pentanediol (MPD) in 100 mM MES buffer (pH 5.7) and equilibrated against a reservoir of the latter solution, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 3.43 64.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 88.39 α = 90 b = 90.53 β = 118.36 c = 85.97 γ = 90
Symmetry Space Group C 1 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 110 CCD ADSC QUANTUM 4 2008-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.9 APS 14-BM-C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.55 50 99.6 0.065 27 6.2 86058 22.5
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) 1.55 1.59 97.4 0.401 3 4.5
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 PDB entry 2OLO 1.55 38.89 85842 4308 99.5 0.225 0.225 0.2089 0.244 0.2097 RANDOM 26.6
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] 1.72 -3.29 0.44 -2.16
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_angle_deg 5.4 c_improper_angle_d 1.48 c_bond_d 0.786 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 25.7 c_angle_deg 5.4 c_improper_angle_d 1.48 c_bond_d 0.786 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot c_mcbond_it c_mcangle_it c_scbond_it c_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3088 Nucleic Acid Atoms Solvent Atoms 416 Heterogen Atoms 86
Software Software Software Name Purpose ADSC data collection CNS refinement DENZO data reduction HKL-2000 data scaling CNS phasing