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The crystal structure of PdxI complex with the Alder-ene adduct
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 MME 550, 0.1M MOPS/HEPES-Na pH 7.5, 0.02M of each alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2-propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol)
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.075 α = 90 b = 86.075 β = 90 c = 291.053 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 EIGER X 16M 2019-04-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.97919 SSRF BL17U1
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 2.396 50 98.83 0.1189 0.135 0.063 0.992 9.58 4.419 43666 34.91
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 2.396 2.482 97.3 0.602 0.68 0.3317 0.787 2.64 4.582
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 2.396 48.219 43642 2182 98.77 0.2006 0.199 0.2002 0.2304 0.2308 35.9831
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 21.178 f_angle_d 0.696 f_chiral_restr 0.048 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7145 Nucleic Acid Atoms Solvent Atoms 237 Heterogen Atoms 50
Software Software Software Name Purpose PHENIX refinement XSCALE data scaling PDB_EXTRACT data extraction XDS data reduction PHENIX phasing