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Structure of C. dubliensis Fdc1 with the prenylated-flavin cofactor in the iminium form.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 0.2 M potassium thiocyanate, sodium acetate pH 5.5 and 15% w/v PEG 4000.
Crystal Properties Matthews coefficient Solvent content 2.47 50.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.97 α = 90 b = 64.55 β = 91.07 c = 96.05 γ = 90
Symmetry Space Group P 1 21 1
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 2014-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.98 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 2.46 67.04 99.8 0.091 6.7 3.4 39186
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 2.46 2.52 99.8 0.48 1.7 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.46 67.04 39186 1956 100 0.20761 0.20514 0.25569 0.2373 RANDOM 26.035
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] -0.01 -0.07 0.26 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.406 r_dihedral_angle_4_deg 22.305 r_dihedral_angle_3_deg 16.611 r_dihedral_angle_1_deg 7.032 r_scangle_it 3.12 r_scbond_it 1.935 r_angle_refined_deg 1.716 r_mcangle_it 1.277 r_angle_other_deg 1.004 r_mcbond_it 0.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.406 r_dihedral_angle_4_deg 22.305 r_dihedral_angle_3_deg 16.611 r_dihedral_angle_1_deg 7.032 r_scangle_it 3.12 r_scbond_it 1.935 r_angle_refined_deg 1.716 r_mcangle_it 1.277 r_angle_other_deg 1.004 r_mcbond_it 0.68 r_mcbond_other 0.206 r_chiral_restr 0.097 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8019 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing