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Structure of A. niger Fdc I327S variant in complex with 2 naphthoic 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 2.37 48.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.642 α = 90 b = 63.592 β = 90 c = 87.741 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 2018-07-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9159 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 1.07 87.74 95.6 0.158 1 6.5 6.5 169880
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 1.07 1.17 73.9 1.127 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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 4ZAA 1.07 87.74 169880 8543 72.058 0.126 0.1243 0.1519 0.1741 12.67
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] 0.363 -0.335 -0.028
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.929 r_dihedral_angle_4_deg 22.231 r_dihedral_angle_3_deg 11.822 r_dihedral_angle_1_deg 6.774 r_rigid_bond_restr 5.293 r_scangle_it 4.531 r_scangle_other 4.53 r_scbond_other 4.072 r_scbond_it 4.071 r_lrange_it 3.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.929 r_dihedral_angle_4_deg 22.231 r_dihedral_angle_3_deg 11.822 r_dihedral_angle_1_deg 6.774 r_rigid_bond_restr 5.293 r_scangle_it 4.531 r_scangle_other 4.53 r_scbond_other 4.072 r_scbond_it 4.071 r_lrange_it 3.888 r_lrange_other 3.443 r_angle_refined_deg 2.148 r_mcangle_other 2.122 r_mcangle_it 2.09 r_mcbond_it 2.046 r_mcbond_other 1.968 r_angle_other_deg 1.676 r_symmetry_nbd_refined 0.33 r_nbd_other 0.292 r_symmetry_xyhbond_nbd_refined 0.29 r_nbd_refined 0.265 r_xyhbond_nbd_refined 0.229 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.18 r_chiral_restr 0.142 r_metal_ion_refined 0.097 r_symmetry_nbtor_other 0.088 r_gen_planes_refined 0.023 r_bond_refined_d 0.02 r_gen_planes_other 0.004 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3850 Nucleic Acid Atoms Solvent Atoms 735 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling