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The structure of a putative haloacid dehalogenase-like family hydrolase from Bacteroides thetaiotaomicron VPI-5482
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 278 0.2M MgCl2, 0.1M HEPES pH7, 25% PEG 3350, 3% D(+) Trehalose dihydrate
, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 2.14 42.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.119 α = 90 b = 104.222 β = 90 c = 121.212 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 CUSTOM-MADE 2007-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97855 APS 19-BM
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 2 50 99.2 0.108 7.2 8.8 31723 31723 -3 26
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 2 2.05 93 0.443 3 5.9 1939
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 2 33.4 31604 31604 1595 99.22 0.179 0.179 0.177 0.1827 0.223 0.2303 RANDOM 24.487
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] 1.29 0.21 -1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_4_deg 12.374 r_dihedral_angle_1_deg 5.828 r_scangle_it 3.959 r_scbond_it 2.687 r_mcangle_it 1.603 r_angle_refined_deg 1.436 r_mcbond_it 1.183 r_angle_other_deg 0.925
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.277 r_dihedral_angle_3_deg 13.769 r_dihedral_angle_4_deg 12.374 r_dihedral_angle_1_deg 5.828 r_scangle_it 3.959 r_scbond_it 2.687 r_mcangle_it 1.603 r_angle_refined_deg 1.436 r_mcbond_it 1.183 r_angle_other_deg 0.925 r_mcbond_other 0.243 r_symmetry_vdw_other 0.242 r_symmetry_vdw_refined 0.223 r_nbd_refined 0.218 r_nbd_other 0.184 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.171 r_chiral_restr 0.087 r_nbtor_other 0.086 r_metal_ion_refined 0.063 r_bond_refined_d 0.015 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 3565 Nucleic Acid Atoms Solvent Atoms 342 Heterogen Atoms 18
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building