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Crystal structure of IpgC in complex with a follow-up compound based on J2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6SCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 30 % PEG 4000, 0.1 M TRIS pH 8.0,
0.3 M magnesium chloride
Crystal Properties Matthews coefficient Solvent content 2.39 48.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.629 α = 90 b = 57.629 β = 90 c = 159.246 γ = 120
Symmetry Space Group P 32 2 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 PIXEL DECTRIS PILATUS 6M 2021-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9184 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.5 50 99.3 0.055 0.999 22.39 10.7 50346 19.69
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.58 0.795 0.911 2.76
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6scb 1.5 31.12 1.36 49972 2498 99.27 0.1979 0.1967 0.197 0.2186 0.2192 27.29
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 19.9239 f_angle_d 0.7797 f_chiral_restr 0.0742 f_bond_d 0.0057 f_plane_restr 0.0054
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2163 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 41
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing Coot model building