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Crystal structure of IRED in complex with NADPH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 298 0.03 M CaCl2, 0.1M MES pH 6.0, 49% v/v PEG 200
Crystal Properties Matthews coefficient Solvent content 2.16 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.831 α = 90 b = 75.831 β = 90 c = 157.008 γ = 120
Symmetry Space Group P 31 2 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 Bruker PHOTON III 2022-10-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.15 36.88 99.3 0.071 14.12 5.64 29044
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.15 2.18 97.6 0.2127 3.14
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.15 36.88 27005 1288 96.86 0.17744 0.17449 0.1828 0.24301 0.2472 RANDOM 26.908
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] 0.05 0.02 0.05 -0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.667 r_dihedral_angle_4_deg 21.784 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 6.465 r_long_range_B_refined 4.873 r_long_range_B_other 4.873 r_scangle_other 3.539 r_mcangle_it 2.68 r_mcangle_other 2.679 r_scbond_it 2.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.667 r_dihedral_angle_4_deg 21.784 r_dihedral_angle_3_deg 15.725 r_dihedral_angle_1_deg 6.465 r_long_range_B_refined 4.873 r_long_range_B_other 4.873 r_scangle_other 3.539 r_mcangle_it 2.68 r_mcangle_other 2.679 r_scbond_it 2.329 r_scbond_other 2.326 r_mcbond_it 1.841 r_mcbond_other 1.841 r_angle_refined_deg 1.519 r_angle_other_deg 1.343 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4208 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 125
Software Software Software Name Purpose REFMAC refinement SAINT data scaling SAINT data reduction PDB_EXTRACT data extraction PHASER phasing