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Structure of a Nitrilotriacetate monooxygenase from Burkholderia pseudomallei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YW1 PDB ENTRY 1YW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 0.2 M sodium acetate, 0.1 M Bis Tris Propane, pH 7.5, 20% PEG3350. 38.61 mg/mL. Cryoprotection 25% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.17 43.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.187 α = 90 b = 92.783 β = 90 c = 162.7 γ = 90
Symmetry Space Group P 21 21 21
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 210 2011-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
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 1.997 48.683 99.5 0.081 10.5 3.3 59660 56755
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 1.95 1.98 99.9 0.368 3.1 6247
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 1YW1 2 48.683 56755 2887 95.12 0.1741 0.172 0.1869 0.2129 0.2277 RANDOM 27.3102
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] -0.15 1.69 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.427 r_dihedral_angle_4_deg 20.626 r_dihedral_angle_3_deg 12.516 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.986 r_scbond_it 1.844 r_angle_refined_deg 1.282 r_mcangle_it 1.19 r_angle_other_deg 0.867 r_mcbond_it 0.657
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.427 r_dihedral_angle_4_deg 20.626 r_dihedral_angle_3_deg 12.516 r_dihedral_angle_1_deg 5.554 r_scangle_it 2.986 r_scbond_it 1.844 r_angle_refined_deg 1.282 r_mcangle_it 1.19 r_angle_other_deg 0.867 r_mcbond_it 0.657 r_mcbond_other 0.157 r_chiral_restr 0.079 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6368 Nucleic Acid Atoms Solvent Atoms 490 Heterogen Atoms 12
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling