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Crystal Structure Analysis of the 2,3-dioxygenase LapB from Pseudomonas in the complex with 4-methylcatechol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native final model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 0.2M ammonium fluoride, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.23 44.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.1 α = 90 b = 97.6 β = 90 c = 133.7 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 2008-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 6C1 1.23985 PAL/PLS 6C1
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 1.94 50 99.9 0.071 35.92 11.5 93774 81556 2
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 1.94 2.01 100 0.754 2.7 10.7 9260
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION AB INITIO PHASING using a random selection of data Native final model 1.94 50 2 81556 73387 8169 78.4 0.244 0.2553 0.278 0.2879 RANDOM 30.394
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] -0.852 0.155 0.697
RMS Deviations Key Refinement Restraint Deviation c_angle_deg 1.88504 c_bond_d 0.012134
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9324 Nucleic Acid Atoms Solvent Atoms 351 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction CNS phasing