☰ Navigation Tabs
Monoclinic Structure of P. aeruginosa LigD phosphoesterase domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9B chain A of PDB entry 3N9B
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 ;Crystallization was carried out in sitting-drop vapor-diffusion setups with 1:1 mixtures of protein solution containing 1.3 mM PaePEC2 and 2mM MnCl2 and reservoir solution containing PEG 5000 monomethylether (MME) (20 - 30%), 100 mM 2-(N-morpholino) ethanesulfonic acid (MES) pH 6.8 - 7.0, 200 mM ammonium sulfate, and 10 mM yttrium (III) chloride at 22 C. , VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.53 51.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.997 α = 90 b = 56.585 β = 118.33 c = 43.503 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 130 IMAGE PLATE RIGAKU RAXIS IV++ Osmic Confocal Mirrors 2010-02-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.54
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 2.3 50 99.7 0.103 12.4 3.9 8818 8792 -3 34
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.3 2.34 99.6 2.97 4 458
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 chain A of PDB entry 3N9B 2.3 28.293 1.34 8730 930 99.7 0.2171 0.2117 0.2063 0.2628 0.2528 10% of data selected at random using CCP4/Unique
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] -8.658 -4.5695 -9.94 16.4482
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.379 f_angle_d 0.638 f_chiral_restr 0.048 f_bond_d 0.002 f_plane_restr 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1187 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 13
Software Software Software Name Purpose HKL-2000 data collection PHASER phasing PHENIX refinement HKL-2000 data reduction SCALEPACK data scaling