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LnmK in complex with 2-sulfonate-propionyl-oxa(dethia)-CoA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HZO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 9% PEG400, 100 mM Bis-Tris pH 7.5, 28% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.35 47.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.087 α = 90 b = 61.087 β = 90 c = 312.986 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 80 IMAGE PLATE MAR scanner 300 mm plate MD2 microdifractometer 2016-02-17 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) 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 1.55 50 99.1 0.261 0.288 91.9 17.9 51370 32.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.61 91.3 1 1 1.1 10.9
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 4HZO 1.55 47.23 48639 2589 99.6 0.181 0.179 0.1898 0.208 0.2144 RANDOM 32.7
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] 0.56 0.28 0.56 -1.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_4_deg 17.202 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.605 r_angle_refined_deg 2.229 r_angle_other_deg 1.483 r_chiral_restr 0.265 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.292 r_dihedral_angle_4_deg 17.202 r_dihedral_angle_3_deg 13.766 r_dihedral_angle_1_deg 6.605 r_angle_refined_deg 2.229 r_angle_other_deg 1.483 r_chiral_restr 0.265 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2377 Nucleic Acid Atoms Solvent Atoms 275 Heterogen Atoms 117
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling PDB_EXTRACT data extraction REFMAC phasing DENZO data reduction