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2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 Protein: 70.0 mg/ml, 0.01M HEPES (pH 7.5), Screen: 0.2M Potassium citrate, 0.3M 3-(1-Pyridinio)-1-propanesulfonate, 20% (w/v) P3350 20%
Crystal Properties Matthews coefficient Solvent content 2.46 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 194.403 α = 90 b = 194.403 β = 90 c = 50.228 γ = 120
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 300 mm CCD C(111) 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rpim I (All) 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 2.05 30 100 0.084 0.084 0.039 20.4 5.6 133171 -3 33.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 100 0.775 0.775 0.38 0.694 2.2 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.05 29.65 126438 6697 99.94 0.19161 0.18964 0.2012 0.22818 0.2344 RANDOM 42.957
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] 0.53 0.27 0.53 -1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.234 r_dihedral_angle_4_deg 10.145 r_dihedral_angle_3_deg 9.424 r_long_range_B_refined 4.91 r_long_range_B_other 4.858 r_scangle_other 3.157 r_mcangle_it 2.324 r_mcangle_other 2.324 r_dihedral_angle_1_deg 2.288 r_scbond_it 2.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.234 r_dihedral_angle_4_deg 10.145 r_dihedral_angle_3_deg 9.424 r_long_range_B_refined 4.91 r_long_range_B_other 4.858 r_scangle_other 3.157 r_mcangle_it 2.324 r_mcangle_other 2.324 r_dihedral_angle_1_deg 2.288 r_scbond_it 2.016 r_scbond_other 2.015 r_mcbond_it 1.499 r_mcbond_other 1.498 r_angle_refined_deg 1.429 r_angle_other_deg 0.881 r_chiral_restr 0.083 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.009 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 14802 Nucleic Acid Atoms Solvent Atoms 669 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHENIX phasing