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Structure of A. niger Fdc WT in complex with FMN and 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 2.34 47.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.628 α = 90 b = 63.183 β = 90 c = 87.318 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 2018-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.90 Diamond I03
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 1.42 64.55 99.3 0.123 1 6.4 4.4 99700
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 1.42 1.44 97.6 0.792 0.6 1.6 4.4
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 1.42 64.481 99668 4919 99.301 0.154 0.1517 0.15 0.1997 0.1981 16.807
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] 0.286 -0.46 0.174
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.728 r_dihedral_angle_4_deg 21.4 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 6.824 r_rigid_bond_restr 4.487 r_lrange_it 4.452 r_lrange_other 4.451 r_scangle_other 3.637 r_scangle_it 3.634 r_scbond_it 3.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.728 r_dihedral_angle_4_deg 21.4 r_dihedral_angle_3_deg 12.256 r_dihedral_angle_1_deg 6.824 r_rigid_bond_restr 4.487 r_lrange_it 4.452 r_lrange_other 4.451 r_scangle_other 3.637 r_scangle_it 3.634 r_scbond_it 3.206 r_scbond_other 3.206 r_mcangle_other 2.849 r_mcangle_it 2.846 r_mcbond_it 2.471 r_mcbond_other 2.46 r_angle_refined_deg 2.006 r_angle_other_deg 1.614 r_symmetry_nbd_refined 0.26 r_nbd_refined 0.244 r_nbd_other 0.24 r_symmetry_xyhbond_nbd_refined 0.227 r_xyhbond_nbd_refined 0.209 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.176 r_chiral_restr 0.119 r_metal_ion_refined 0.093 r_symmetry_nbtor_other 0.085 r_symmetry_metal_ion_refined 0.053 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3804 Nucleic Acid Atoms Solvent Atoms 464 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling