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Structure of E282Q A. niger Fdc1 in complex with pentafluoro-cinnamic acid
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4ZA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.42 49.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.24 α = 90 b = 64.33 β = 90 c = 88.1 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 PILATUS3 S 6M 2014-02-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 .92 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.18 44.05 98 17.08 6.2 175886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.18 1.222 0.6343 3.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZA4 1.18 44.05 167083 8802 97.96 0.14182 0.14097 0.15765 0.1639 RANDOM 12.885
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] -0.17 0.57 -0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 21.692 r_long_range_B_other 13.382 r_long_range_B_refined 13.337 r_dihedral_angle_3_deg 12.221 r_dihedral_angle_1_deg 6.493 r_scangle_other 3.55 r_angle_refined_deg 2.632 r_scbond_other 2.592 r_scbond_it 2.587
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.225 r_dihedral_angle_4_deg 21.692 r_long_range_B_other 13.382 r_long_range_B_refined 13.337 r_dihedral_angle_3_deg 12.221 r_dihedral_angle_1_deg 6.493 r_scangle_other 3.55 r_angle_refined_deg 2.632 r_scbond_other 2.592 r_scbond_it 2.587 r_mcangle_it 1.772 r_mcangle_other 1.772 r_mcbond_it 1.257 r_mcbond_other 1.256 r_angle_other_deg 1.245 r_chiral_restr 0.155 r_bond_refined_d 0.03 r_gen_planes_refined 0.016 r_bond_other_d 0.006 r_gen_planes_other 0.004 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 3847 Nucleic Acid Atoms Solvent Atoms 729 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing