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Structure of A. niger Fdc WT in complex with benzothiophene 2 carboxylic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZAA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.41 48.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.72 α = 90 b = 63.611 β = 90 c = 87.627 γ = 90
Symmetry Space Group P 21 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 DECTRIS PILATUS 6M-F 2018-06-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.916 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.02 45.378 96.5 0.077 1 10.1 5.2 218173
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.02 1.09 71.7 0.785 0.7 1.6
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4ZAA 1.021 45.378 218173 10900 80.725 0.123 0.1225 0.1227 0.1417 0.1418 13.054
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] 0.074 -0.246 0.172
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.774 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 11.482 r_rigid_bond_restr 10.229 r_dihedral_angle_1_deg 6.851 r_scbond_it 4.839 r_scbond_other 4.838 r_scangle_it 4.767 r_scangle_other 4.766 r_lrange_it 4.746
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.774 r_dihedral_angle_4_deg 20.451 r_dihedral_angle_3_deg 11.482 r_rigid_bond_restr 10.229 r_dihedral_angle_1_deg 6.851 r_scbond_it 4.839 r_scbond_other 4.838 r_scangle_it 4.767 r_scangle_other 4.766 r_lrange_it 4.746 r_lrange_other 4.746 r_mcangle_other 3.392 r_mcangle_it 3.391 r_mcbond_it 2.678 r_mcbond_other 2.668 r_angle_refined_deg 2.276 r_angle_other_deg 1.689 r_nbd_refined 0.313 r_symmetry_xyhbond_nbd_refined 0.302 r_xyhbond_nbd_refined 0.262 r_nbd_other 0.244 r_symmetry_nbd_refined 0.228 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.183 r_chiral_restr 0.151 r_symmetry_xyhbond_nbd_other 0.124 r_symmetry_nbtor_other 0.092 r_metal_ion_refined 0.088 r_gen_planes_refined 0.024 r_bond_refined_d 0.023 r_gen_planes_other 0.006 r_bond_other_d 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3852 Nucleic Acid Atoms Solvent Atoms 630 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling