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Structure of E277D A. niger Fdc1 with prFMN in the hydroxylated form
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 2.37 48.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.91 α = 90 b = 63.46 β = 90 c = 87.72 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 2015-10-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.987 Diamond I03
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 64.73 99 7.21 4.4 65903
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 1.295 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 (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 64.73 62666 3236 99.43 0.16767 0.16578 0.1802 0.20494 0.2142 RANDOM 17.411
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] -0.62 0.95 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 20.744 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.55 r_long_range_B_refined 4.77 r_long_range_B_other 4.77 r_scangle_other 2.819 r_scbond_other 1.898 r_scbond_it 1.897 r_angle_refined_deg 1.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.823 r_dihedral_angle_4_deg 20.744 r_dihedral_angle_3_deg 12.511 r_dihedral_angle_1_deg 6.55 r_long_range_B_refined 4.77 r_long_range_B_other 4.77 r_scangle_other 2.819 r_scbond_other 1.898 r_scbond_it 1.897 r_angle_refined_deg 1.896 r_mcangle_it 1.833 r_mcangle_other 1.833 r_mcbond_it 1.305 r_mcbond_other 1.303 r_angle_other_deg 1.082 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002 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 3814 Nucleic Acid Atoms Solvent Atoms 563 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing