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E. coli IspH crystallized in the presence of adenosine hemisulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4MUY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 27.5% (w/v) PEG 3350, 150 mM (NH4)2SO4, 100 mM Bis-Tris pH 6.5, 5 mM adenosine hemisulfate
Crystal Properties Matthews coefficient Solvent content 2.16 42.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.909 α = 90 b = 81.291 β = 90 c = 112.871 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 EIGER2 X 16M 2024-03-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.033420 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.85 47.361 99.4 0.292 0.315 0.117 0.996 7.9 13.5 53566
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.89 99.1 2.517 2.713 1.008 0.63 1.4 13.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT NONE 1.852 47.361 53500 2784 99.225 0.211 0.2084 0.2039 0.2533 0.2497 26.429
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] -1.108 -1.252 2.359
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.599 r_dihedral_angle_6_deg 14.732 r_dihedral_angle_2_deg 8.813 r_lrange_other 6.985 r_lrange_it 6.984 r_dihedral_angle_1_deg 6.149 r_scangle_other 5.846 r_scangle_it 5.844 r_scbond_it 3.714 r_scbond_other 3.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.599 r_dihedral_angle_6_deg 14.732 r_dihedral_angle_2_deg 8.813 r_lrange_other 6.985 r_lrange_it 6.984 r_dihedral_angle_1_deg 6.149 r_scangle_other 5.846 r_scangle_it 5.844 r_scbond_it 3.714 r_scbond_other 3.71 r_mcangle_it 3.154 r_mcangle_other 3.153 r_mcbond_it 2.18 r_mcbond_other 2.178 r_angle_refined_deg 1.837 r_angle_other_deg 0.628 r_nbd_other 0.256 r_nbd_refined 0.219 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.191 r_symmetry_nbd_refined 0.187 r_nbtor_refined 0.172 r_metal_ion_refined 0.133 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4920 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Coot model building XDS data reduction Aimless data scaling MOLREP phasing