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Crystal structure of Putative haloacid dehalogenase-like hydrolase from Bacteroides fragilis
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 289 1.0 M Sodium phosphate pH5.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.59 52.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.62 α = 90 b = 62.62 β = 90 c = 133.913 γ = 90
Symmetry Space Group P 41 21 2
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 2008-04-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97857 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 99.7 0.103 27.52 9.6 8776 18723 -3 24
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 2.02 100 0.428 3.17 6.5 465
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 50 18404 18404 940 98.18 0.19975 0.19975 0.19786 0.198 0.235 0.2344 RANDOM 29.087
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] 1.44 1.44 -2.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 17.862 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 8.75 r_scangle_it 2.931 r_scbond_it 2.021 r_angle_refined_deg 1.525 r_mcangle_it 1.138 r_mcbond_it 0.74 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.542 r_dihedral_angle_4_deg 17.862 r_dihedral_angle_3_deg 14.759 r_dihedral_angle_1_deg 8.75 r_scangle_it 2.931 r_scbond_it 2.021 r_angle_refined_deg 1.525 r_mcangle_it 1.138 r_mcbond_it 0.74 r_nbtor_refined 0.306 r_symmetry_vdw_refined 0.215 r_nbd_refined 0.209 r_xyhbond_nbd_refined 0.18 r_symmetry_hbond_refined 0.174 r_chiral_restr 0.12 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 1658 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing