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Structure of E277Q A. niger fdc1 in complex with a phenylpyruvate derived adduct to the prenylated flavin cofactor
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 2.38 48.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.27 α = 90 b = 63.73 β = 90 c = 87.42 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 2014-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 1.000 Diamond I02
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 1.64 53.14 100 11.51 5.5 66447
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 1.64 1.699 0.778 5.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZA4 1.64 53.14 63072 3376 99.78 0.1474 0.14585 0.1459 0.17618 0.1753 RANDOM 16.208
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] -0.48 0.74 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 21.235 r_dihedral_angle_3_deg 12.09 r_long_range_B_refined 6.523 r_long_range_B_other 6.522 r_dihedral_angle_1_deg 6.408 r_scangle_other 3.73 r_scbond_it 2.583 r_scbond_other 2.582 r_angle_refined_deg 2.127
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.56 r_dihedral_angle_4_deg 21.235 r_dihedral_angle_3_deg 12.09 r_long_range_B_refined 6.523 r_long_range_B_other 6.522 r_dihedral_angle_1_deg 6.408 r_scangle_other 3.73 r_scbond_it 2.583 r_scbond_other 2.582 r_angle_refined_deg 2.127 r_mcangle_it 2.075 r_mcangle_other 2.07 r_mcbond_it 1.497 r_mcbond_other 1.493 r_angle_other_deg 1.185 r_chiral_restr 0.146 r_bond_refined_d 0.022 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.003 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 555 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing