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Apo FdhC- a nucleotide-linked sugar GNAT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Lab Model from SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 2.5 M AmSo4, 2% DMSO, 100 mM HEPPS
Crystal Properties Matthews coefficient Solvent content 2.29 46.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.549 α = 90 b = 69.549 β = 90 c = 137.85 γ = 120
Symmetry Space Group P 63 2 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 2015-08-09 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 1.89 50 98 0.08 17.1 6.9 16130
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 Lab Model from SAD 1.89 50 15290 817 98.01 0.19762 0.1946 0.2039 0.2581 0.2685 RANDOM 24.496
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] 0.25 0.13 0.25 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_4_deg 20.337 r_dihedral_angle_3_deg 16.626 r_long_range_B_refined 6.37 r_long_range_B_other 6.369 r_dihedral_angle_1_deg 6.321 r_scangle_other 4.841 r_mcangle_it 3.343 r_mcangle_other 3.342 r_scbond_it 3.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.478 r_dihedral_angle_4_deg 20.337 r_dihedral_angle_3_deg 16.626 r_long_range_B_refined 6.37 r_long_range_B_other 6.369 r_dihedral_angle_1_deg 6.321 r_scangle_other 4.841 r_mcangle_it 3.343 r_mcangle_other 3.342 r_scbond_it 3.144 r_scbond_other 3.142 r_mcbond_it 2.252 r_mcbond_other 2.217 r_angle_refined_deg 1.846 r_angle_other_deg 1.064 r_chiral_restr 0.128 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 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 1478 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement SADABS data scaling SAINT data reduction PHASER phasing