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The structure of PdxI in complex with its substrate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 10% PEG 20000, 20% PEG MME550, 0.02M of each alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol), 0.1M MOPS/HEPES-Na pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.64 53.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.345 α = 90 b = 86.345 β = 90 c = 292.078 γ = 90
Symmetry Space Group P 41 21 2
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 PILATUS3 6M 2018-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.9793 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.99 50 100 0.163 0.166 0.032 3.8 26.3 77183 24.65
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 1.99 2.02 100 0.988 1.008 0.2 0.882 25.3
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 THROUGHOUT 7BQJ 1.99 38.615 1.34 76827 3852 99.67 0.1757 0.1743 0.1754 0.2021 0.2036 24.7415
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 5.02 f_angle_d 0.991 f_chiral_restr 0.083 f_bond_d 0.013 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7186 Nucleic Acid Atoms Solvent Atoms 620 Heterogen Atoms 94
Software Software Software Name Purpose PHENIX refinement HKL-3000 data scaling PDB_EXTRACT data extraction HKL-3000 data reduction PHENIX phasing