☰ Navigation Tabs
X-ray crystallographic structure of KstA15, polyketide biosynthesis enzyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2GEX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.75 293 0.1 M Bis-TRIS-Propane pH 7.75, 2.2 M ammonium-sulfate
Crystal Properties Matthews coefficient Solvent content 1.99 34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.975 α = 90 b = 52.751 β = 90 c = 108.162 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 110 PIXEL DECTRIS PILATUS 2M MIRRORS 2018-11-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87313 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.1 44.61 100 0.097 0.063 0.998 11.4 6.1 17018 2 56.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.1 2.16 100 0.804 0.532 0.732 2 5.9
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 MOLECULAR REPLACEMENT THROUGHOUT 2.1 44.61 16150 821 99.92 0.18707 0.18487 0.1949 0.23091 0.2338 RANDOM 34.32
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] 1.05 -0.51 -0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.107 r_dihedral_angle_4_deg 16.547 r_dihedral_angle_3_deg 16.365 r_long_range_B_refined 7.268 r_long_range_B_other 7.267 r_dihedral_angle_1_deg 6.559 r_scangle_other 5.885 r_scbond_it 3.778 r_scbond_other 3.777 r_mcangle_it 3.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.107 r_dihedral_angle_4_deg 16.547 r_dihedral_angle_3_deg 16.365 r_long_range_B_refined 7.268 r_long_range_B_other 7.267 r_dihedral_angle_1_deg 6.559 r_scangle_other 5.885 r_scbond_it 3.778 r_scbond_other 3.777 r_mcangle_it 3.746 r_mcangle_other 3.744 r_mcbond_it 2.602 r_mcbond_other 2.598 r_angle_refined_deg 1.516 r_angle_other_deg 1.286 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 2274 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing