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Imine reductase RedE bound with NADP+ and arcyriaflavin A (primary site)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other selenomethionine-substituted RedE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 0.33 M NaI,
0.1 M Tris-HCl pH 8.5,
23 % PEG 3350,
1.5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.93 57.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.114 α = 90 b = 110.767 β = 107.598 c = 66.987 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2018-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.979 SSRL BL9-2
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 1.6 37.75 96.6 0.073 0.078 0.029 0.999 14.4 7.1 95462 17.91
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 1.6 1.63 0.887 0.957 0.355 0.845 2.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.6 37.75 1.34 95375 2000 96.43 0.1559 0.1552 0.1552 0.1889 0.1897 26.33
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 12.0054 f_angle_d 1.2722 f_chiral_restr 0.0716 f_plane_restr 0.0105 f_bond_d 0.0102
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4193 Nucleic Acid Atoms Solvent Atoms 762 Heterogen Atoms 202
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building