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Structure of A. niger Fdc1 with the prenylated-flavin cofactor in the iminium form.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 Initial screening of 0.3 microl 14 mg/ml A. niger Fdc1 in 100 mM NaCl, 25 mM Tris pH 7.5 and 0.3 microl reservoir solution at 4C resulted in a number of hits including PACT condition F4 (molecular dimensions). Seed stock produced from these crystals was used in an optimization screen based around 0.2 M potassium thiocyanate, Bis-Tris propane 6.5, 20 % w/v PEG 3350 mixing 0.05 microl seed stock, 0.25 microl protein solution and 0.3 microl reservoir solution at 4C.
Crystal Properties Matthews coefficient Solvent content 2.39 48.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.99 α = 90 b = 63.93 β = 90 c = 87.63 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 PSI PILATUS 6M 2014-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.987 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.22 33.82 99.96 0.037 11.2 6.1 152260
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.22 1.25 99.99 0.354 2 5.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.22 33.82 152260 8041 99.96 0.14652 0.14573 0.1473 0.16111 0.1624 RANDOM 9.809
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] 1.04 -2.27 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 21.066 r_dihedral_angle_3_deg 12.311 r_mcbond_other 7.517 r_dihedral_angle_1_deg 6.603 r_scangle_it 6.569 r_rigid_bond_restr 5.09 r_scbond_it 4.873 r_angle_other_deg 4.393 r_mcangle_it 3.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.569 r_dihedral_angle_4_deg 21.066 r_dihedral_angle_3_deg 12.311 r_mcbond_other 7.517 r_dihedral_angle_1_deg 6.603 r_scangle_it 6.569 r_rigid_bond_restr 5.09 r_scbond_it 4.873 r_angle_other_deg 4.393 r_mcangle_it 3.096 r_angle_refined_deg 2.384 r_mcbond_it 2.338 r_chiral_restr 0.158 r_bond_refined_d 0.028 r_gen_planes_other 0.02 r_gen_planes_refined 0.018 r_bond_other_d 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3847 Nucleic Acid Atoms Solvent Atoms 447 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing