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Crystal structure of Pseudomonas aeruginosa IspD in complex with C8H8N2O
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 26% PEG 500MME
100 mM MES pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.33 47.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.41 α = 90 b = 75.59 β = 104.761 c = 37.8 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 DECTRIS EIGER R 4M 2023-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE MASSIF-3 0.9677 ESRF MASSIF-3
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 2.17 44.2 96 0.06137 0.07204 0.03746 0.996 10.01 3.6 12788 59.23
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 2.17 2.39 88.62 0.6201 0.7483 0.4111 0.843 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.17 44.2 1.38 12711 599 95.98 0.1996 0.1979 0.2354 0.2679 58.85
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 20.1074 f_angle_d 0.4806 f_chiral_restr 0.0388 f_plane_restr 0.0044 f_bond_d 0.0021
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1751 Nucleic Acid Atoms Solvent Atoms 50 Heterogen Atoms 11
Software Software Software Name Purpose PHENIX refinement XDS data reduction XSCALE data scaling PHASER phasing