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Crystal structure of E282Q 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 48.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.02 α = 90 b = 63.51 β = 90 c = 87.62 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 2017-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976 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 1.28 38.3 96 8.81 4.5 133397
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 1.28 1.326 1.535 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4ZA4 1.28 38.3 126774 6623 96.53 0.16711 0.16591 0.19027 0.2007 RANDOM 15.985
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] -0.7 1.32 -0.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 21.266 r_dihedral_angle_3_deg 12.285 r_long_range_B_other 10.422 r_long_range_B_refined 10.419 r_dihedral_angle_1_deg 6.44 r_scangle_other 3.772 r_scbond_it 2.608 r_scbond_other 2.608 r_angle_refined_deg 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.574 r_dihedral_angle_4_deg 21.266 r_dihedral_angle_3_deg 12.285 r_long_range_B_other 10.422 r_long_range_B_refined 10.419 r_dihedral_angle_1_deg 6.44 r_scangle_other 3.772 r_scbond_it 2.608 r_scbond_other 2.608 r_angle_refined_deg 2.375 r_mcangle_it 2.031 r_mcangle_other 2.031 r_mcbond_it 1.445 r_mcbond_other 1.445 r_angle_other_deg 1.19 r_chiral_restr 0.299 r_bond_refined_d 0.024 r_gen_planes_refined 0.014 r_gen_planes_other 0.004 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 3847 Nucleic Acid Atoms Solvent Atoms 597 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling REFMAC phasing