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Crystal structure of the LpqC, poly(3-hydroxybutyrate) depolymerase from Bordetella parapertussis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 289 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5, 10% Dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.36 47.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.879 α = 90 b = 83.71 β = 92.68 c = 90.792 γ = 90
Symmetry Space Group P 1 21 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 Mirrors 2008-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 1.83 41.83 99.8 0.12 8.5 4.5 54978 54978 20.67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.83 1.86 99.7 0.598 2 3.8 2697
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.83 41.83 52230 52230 2803 99.69 0.166 0.166 0.164 0.1636 0.209 0.2089 RANDOM 24.02
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] -0.88 -0.37 1.35 -0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 19.518 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_1_deg 6.211 r_scangle_it 4.704 r_scbond_it 3.075 r_mcangle_it 1.705 r_angle_refined_deg 1.639 r_mcbond_it 1.077 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.634 r_dihedral_angle_4_deg 19.518 r_dihedral_angle_3_deg 15.257 r_dihedral_angle_1_deg 6.211 r_scangle_it 4.704 r_scbond_it 3.075 r_mcangle_it 1.705 r_angle_refined_deg 1.639 r_mcbond_it 1.077 r_nbtor_refined 0.309 r_symmetry_vdw_refined 0.237 r_nbd_refined 0.207 r_symmetry_hbond_refined 0.182 r_xyhbond_nbd_refined 0.162 r_chiral_restr 0.119 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4530 Nucleic Acid Atoms Solvent Atoms 439 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing MLPHARE phasing DM phasing SHELXD phasing RESOLVE phasing Coot model building