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Structure of A. niger Fdc WT in complex with indol-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 2.42 49.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.781 α = 90 b = 63.725 β = 90 c = 87.707 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 2018-02-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.975 Diamond I04
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 1.12 64.79 99.5 0.093 1 9.3 6 204931
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 1.12 1.14 91.9 0.739 0.5 1.5
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 1.12 64.685 202805 10012 98.513 0.141 0.1397 0.1397 0.1686 0.1693 12.659
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] -0.022 -0.149 0.171
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 21.99 r_dihedral_angle_3_deg 11.803 r_dihedral_angle_1_deg 6.783 r_rigid_bond_restr 5.227 r_lrange_it 4.183 r_lrange_other 4.183 r_scangle_other 3.633 r_scangle_it 3.632 r_scbond_it 3.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.405 r_dihedral_angle_4_deg 21.99 r_dihedral_angle_3_deg 11.803 r_dihedral_angle_1_deg 6.783 r_rigid_bond_restr 5.227 r_lrange_it 4.183 r_lrange_other 4.183 r_scangle_other 3.633 r_scangle_it 3.632 r_scbond_it 3.117 r_scbond_other 3.117 r_angle_refined_deg 2.224 r_mcangle_other 2.194 r_mcangle_it 2.191 r_mcbond_it 2.014 r_mcbond_other 2.004 r_angle_other_deg 1.686 r_symmetry_xyhbond_nbd_refined 0.302 r_nbd_refined 0.254 r_xyhbond_nbd_other 0.231 r_nbd_other 0.225 r_xyhbond_nbd_refined 0.22 r_symmetry_nbd_refined 0.212 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.181 r_chiral_restr 0.149 r_metal_ion_refined 0.092 r_symmetry_nbtor_other 0.09 r_gen_planes_refined 0.024 r_bond_refined_d 0.02 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3852 Nucleic Acid Atoms Solvent Atoms 656 Heterogen Atoms 64
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling