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Imine reductase RedE bound with NADP+ and arcyriaflavin A (secondary 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,
21 % PEG 3350,
1.5 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.99 58.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.588 α = 90 b = 111.529 β = 108.467 c = 67.695 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 0.97946 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 1.63 37.94 98.7 0.071 0.077 0.03 0.998 12.8 6.9 93667 23.02
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 1.63 1.67 97.9 0.665 0.722 0.276 0.948 2.3 6.7
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 1.63 36.6 1.33 93448 1708 98.48 0.1942 0.1937 0.2207 0.2331 34.41
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 11.9976 f_angle_d 0.7431 f_chiral_restr 0.0446 f_plane_restr 0.006 f_bond_d 0.0052
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4063 Nucleic Acid Atoms Solvent Atoms 586 Heterogen Atoms 178
Software Software Software Name Purpose PHENIX refinement Blu-Ice data collection XDS data reduction Aimless data scaling PHASER phasing Coot model building