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Crystal Structure of CbAR mutant (H162F) in complex with NADP+ and a bulky 1,3-cyclodiketone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 291 0.1 M HEPES pH 7.5, 15% isopropanol and 19% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.17 43.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 124.92 α = 90 b = 124.92 β = 90 c = 133.778 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 Bruker PHOTON II 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER D8 QUEST 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.75 24.11 99.8 0.983 7.9 6.8 26700
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.846 0.23
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 7YB1 2.75 24.11 26700 1383 99.72 0.20806 0.2048 0.2176 0.27012 0.2764 RANDOM 19.907
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] 0.67 0.67 -1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.081 r_dihedral_angle_4_deg 18.765 r_dihedral_angle_3_deg 17.222 r_dihedral_angle_1_deg 8.338 r_long_range_B_refined 4.202 r_long_range_B_other 4.202 r_scangle_other 2.289 r_mcangle_it 2.162 r_mcangle_other 2.162 r_angle_refined_deg 1.654
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.081 r_dihedral_angle_4_deg 18.765 r_dihedral_angle_3_deg 17.222 r_dihedral_angle_1_deg 8.338 r_long_range_B_refined 4.202 r_long_range_B_other 4.202 r_scangle_other 2.289 r_mcangle_it 2.162 r_mcangle_other 2.162 r_angle_refined_deg 1.654 r_scbond_other 1.369 r_scbond_it 1.367 r_mcbond_it 1.299 r_mcbond_other 1.299 r_angle_other_deg 1.268 r_chiral_restr 0.068 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 7659 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 224
Software Software Software Name Purpose SAINT data scaling REFMAC refinement SAINT data reduction MOLREP phasing