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Structure of a putative lipolytic protein of G-D-S-L family from Desulfitobacterium hafniense DCB-2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M Potassium Thiocyanate, 30% PEG MME 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.997 α = 90 b = 63.649 β = 90 c = 85.647 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 MARMOSAIC 225 mm CCD beryllium lenses 2014-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
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 2.19 85.65 98.9 0.199 13.6 13.6 29332 29332 -3
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 2.19 2.4 95.6 0.84 3 11.1
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 (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 2.19 30 27798 27798 1480 98.72 0.20269 0.19914 0.2076 0.26994 0.2691 RANDOM 23.771
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] -0.91 0.66 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.065 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_4_deg 4.921 r_long_range_B_refined 4.708 r_long_range_B_other 4.586 r_dihedral_angle_1_deg 2.841 r_scangle_other 2.163 r_angle_refined_deg 1.814 r_scbond_it 1.39 r_scbond_other 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.065 r_dihedral_angle_3_deg 11.182 r_dihedral_angle_4_deg 4.921 r_long_range_B_refined 4.708 r_long_range_B_other 4.586 r_dihedral_angle_1_deg 2.841 r_scangle_other 2.163 r_angle_refined_deg 1.814 r_scbond_it 1.39 r_scbond_other 1.39 r_mcangle_it 1.363 r_mcangle_other 1.362 r_mcbond_it 0.902 r_mcbond_other 0.902 r_angle_other_deg 0.86 r_chiral_restr 0.11 r_gen_planes_refined 0.024 r_gen_planes_other 0.019 r_bond_refined_d 0.013 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4116 Nucleic Acid Atoms Solvent Atoms 311 Heterogen Atoms 2
Software Software Software Name Purpose Blu-Ice data collection PHENIX model building REFMAC refinement HKL-2000 data reduction Aimless data scaling PHENIX phasing