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Crystal Structure of anthrol reductase (CbAR) in complex with NADP+ and emodin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IS3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 0.1 M HEPES pH 7.5, 15% isopropanol and 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.17 43.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.797 α = 90 b = 123.362 β = 90 c = 126.111 γ = 90
Symmetry Space Group P 2 21 21
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 PILATUS3 6M 2019-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NFPSS BEAMLINE BL19U1 0.979 NFPSS BL19U1
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 1.85 50 99.1 0.999 8.3 12.1 89048
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 1.85 1.88 90.3 0.569 7.1
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 3IS3 1.85 45.89 84089 4568 98.31 0.15285 0.15096 0.1634 0.18763 0.198 RANDOM 19.871
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] 0.09 -0.04 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.44 r_dihedral_angle_4_deg 15.119 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_1_deg 7.005 r_long_range_B_refined 5.382 r_long_range_B_other 5.382 r_scangle_other 4.053 r_scbond_it 2.709 r_scbond_other 2.708 r_mcangle_it 2.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.44 r_dihedral_angle_4_deg 15.119 r_dihedral_angle_3_deg 12.889 r_dihedral_angle_1_deg 7.005 r_long_range_B_refined 5.382 r_long_range_B_other 5.382 r_scangle_other 4.053 r_scbond_it 2.709 r_scbond_other 2.708 r_mcangle_it 2.634 r_mcangle_other 2.633 r_mcbond_it 1.825 r_mcbond_other 1.825 r_angle_refined_deg 1.759 r_angle_other_deg 1.481 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 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 7907 Nucleic Acid Atoms Solvent Atoms 569 Heterogen Atoms 296
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing