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FdhC with bound products: Coenzyme A and dTDP-3-amino-3,6-dideoxy-d-glucose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 5 277 30% monomethylether poly(ethylene glycol) 5000, 200 mM LiCl, and 100 mM Homo-PIPES
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.812 α = 90 b = 75.812 β = 90 c = 73.537 γ = 90
Symmetry Space Group P 41 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 CCD Bruker Platinum 135 2014-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.9 50 99.7 0.108 21.1 29.5 17505
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 5kta 1.9 50 16577 880 99.74 0.20419 0.20082 0.2092 0.269 0.2722 RANDOM 23.168
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] 0.83 0.83 -1.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.126 r_dihedral_angle_4_deg 18.993 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_1_deg 7.529 r_long_range_B_refined 5.367 r_long_range_B_other 5.366 r_scangle_other 4.024 r_mcangle_it 3.27 r_mcangle_other 3.269 r_scbond_it 2.482
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.126 r_dihedral_angle_4_deg 18.993 r_dihedral_angle_3_deg 15.884 r_dihedral_angle_1_deg 7.529 r_long_range_B_refined 5.367 r_long_range_B_other 5.366 r_scangle_other 4.024 r_mcangle_it 3.27 r_mcangle_other 3.269 r_scbond_it 2.482 r_scbond_other 2.481 r_mcbond_it 2.096 r_mcbond_other 2.093 r_angle_refined_deg 1.929 r_angle_other_deg 1.042 r_chiral_restr 0.112 r_bond_refined_d 0.017 r_gen_planes_refined 0.008 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1570 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement SAINT data reduction SADABS data scaling PHASER phasing