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IspG in complex with Epoxide Intermediate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4S38
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M BIS-TRIS PROPANE; 20% PEG3350; 0.2 M Na2SO4 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.93 α = 90 b = 62.84 β = 127.02 c = 86.2 γ = 90
Symmetry Space Group C 1 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 PSI PILATUS 6M 2014-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.971 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.45 30 97.1 0.037 14.9 3 84126 81686 2 2
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 1.45 1.55 97.7 0.481 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4S38 1.45 10 81684 77599 4085 97.43 0.12498 0.12305 0.1212 0.16103 0.1594 RANDOM 26.71
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] -0.02 -0.05 0.23 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_sphericity_free 29.853 r_dihedral_angle_4_deg 19.59 r_sphericity_bonded 17.898 r_dihedral_angle_3_deg 14.081 r_scangle_other 7.315 r_scbond_it 7.011 r_long_range_B_refined 6.617 r_long_range_B_other 6.617 r_scbond_other 6.568
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.68 r_sphericity_free 29.853 r_dihedral_angle_4_deg 19.59 r_sphericity_bonded 17.898 r_dihedral_angle_3_deg 14.081 r_scangle_other 7.315 r_scbond_it 7.011 r_long_range_B_refined 6.617 r_long_range_B_other 6.617 r_scbond_other 6.568 r_rigid_bond_restr 6.176 r_dihedral_angle_1_deg 5.724 r_mcangle_it 4.784 r_mcangle_other 4.572 r_mcbond_it 4.071 r_mcbond_other 4.034 r_angle_refined_deg 2.778 r_angle_other_deg 1.485 r_chiral_restr 0.207 r_bond_refined_d 0.024 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3076 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 30
Software Software Software Name Purpose XDS data scaling REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing