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1.35 Angstrom Crystal Structure of C-terminal Domain of Glycosyl Transferase Group 1 Family Protein (LpcC) from Francisella tularensis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3C4Q PDB-3C4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 292 Protein: 10.4 mg/ml, 0.01M Tris-HCL (pH 8.3);
Screen: PACT (D6), 0.1M MMT buffer (pH 9.0), 25% (w/v) PEG 1500.
Crystal Properties Matthews coefficient Solvent content 1.73 29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.484 α = 90 b = 58.962 β = 117.65 c = 41.646 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 MARMOSAIC 225 mm CCD C(111) 2016-02-08 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) R Sym I (Observed) CC (Half) 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 1.35 30 99.7 0.073 0.073 0.811 35.5 4.9 36249 -3 15.5
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 1.35 1.37 98.9 0.66 2.6 4.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB-3C4Q 1.35 29.55 34441 1654 99.65 0.16355 0.16157 0.1612 0.20303 0.2029 RANDOM 16.506
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] 0.84 -0.27 -0.95 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_4_deg 18.774 r_dihedral_angle_3_deg 12.567 r_long_range_B_refined 5.485 r_long_range_B_other 5.242 r_dihedral_angle_1_deg 4.486 r_scangle_other 1.634 r_angle_refined_deg 1.56 r_mcangle_it 1.187 r_mcangle_other 1.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.363 r_dihedral_angle_4_deg 18.774 r_dihedral_angle_3_deg 12.567 r_long_range_B_refined 5.485 r_long_range_B_other 5.242 r_dihedral_angle_1_deg 4.486 r_scangle_other 1.634 r_angle_refined_deg 1.56 r_mcangle_it 1.187 r_mcangle_other 1.186 r_scbond_it 1.04 r_scbond_other 1.039 r_angle_other_deg 0.901 r_mcbond_it 0.717 r_mcbond_other 0.71 r_chiral_restr 0.1 r_gen_planes_refined 0.023 r_gen_planes_other 0.019 r_bond_refined_d 0.011 r_bond_other_d 0.002 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 1544 Nucleic Acid Atoms Solvent Atoms 269 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling MoRDa phasing