☰ Navigation Tabs
Streptococcus pneumonia TIGR4 flavodoxin: structural and biophysical characterization of a novel drug target
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5LJI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 292 100mM Bis-Tris pH 5.5 and 200 mM calcium chloride, and 10% glycerol
Crystal Properties Matthews coefficient Solvent content 1.73 29.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 29.871 α = 90 b = 60.707 β = 90 c = 61.803 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 PIXEL DECTRIS PILATUS3 S 6M 2013-05-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 20 99.2 0.102 0.998 13.9 9.9 15310
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 5Lji 1.6 61.8 14837 433 98.92 0.17375 0.17257 0.1868 0.21532 0.2306 RANDOM 16.596
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] 2 -0.49 -1.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 31.757 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 5.925 r_long_range_B_refined 5.662 r_long_range_B_other 5.624 r_scangle_other 5.047 r_scbond_other 3.329 r_scbond_it 3.321 r_mcangle_other 2.279
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.018 r_dihedral_angle_4_deg 31.757 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 5.925 r_long_range_B_refined 5.662 r_long_range_B_other 5.624 r_scangle_other 5.047 r_scbond_other 3.329 r_scbond_it 3.321 r_mcangle_other 2.279 r_mcangle_it 2.261 r_angle_refined_deg 1.874 r_mcbond_it 1.5 r_mcbond_other 1.462 r_angle_other_deg 1.16 r_chiral_restr 0.168 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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 1121 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing