☰ Navigation Tabs
Crystal structures of AKR1C3 ternary complex with NADP+ and the chromene derivative 2j
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7C7F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 25-30% (w/v) polyethylene glycol 3350 (PEG3350), 200 mM sodium acetate and 100 mM cacodylate, pH 6.6
Crystal Properties Matthews coefficient Solvent content 2.07 40.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.121 α = 77.254 b = 52.314 β = 86.161 c = 76.683 γ = 77.639
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 2019-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.86 46.3 96.69 0.0771 0.09217 0.98 8.54 3.4 47898 33.98
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.86 1.92 0.8058 0.9581 0.663
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 FREE R-VALUE 7C7F 1.86 46.3 1.97 47898 2322 96.69 0.2214 0.2192 0.2201 0.265 0.2656 42.74
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 24.989 f_angle_d 1.1871 f_chiral_restr 0.0803 f_bond_d 0.0083 f_plane_restr 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5158 Nucleic Acid Atoms Solvent Atoms 315 Heterogen Atoms 70
Software Software Software Name Purpose PHENIX refinement REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing