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Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum: lysine-dimethylated form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 24% (W/V) PEG 3350, 0.1M HEPES PH 7.5, 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE
Crystal Properties Matthews coefficient Solvent content 2.3 46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.76 α = 90 b = 136.16 β = 90 c = 171.68 γ = 90
Symmetry Space Group P 2 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210r 2011-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 2.07 42.66 99.6 0.051 22.3 7 83053
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.07 2.12 98.4 0.245 7.2 6.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 2.07 40.93 78808 4180 99.47 0.18839 0.18561 0.1935 0.24177 0.2456 RANDOM 38.583
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] 0.91 1.63 -2.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.656 r_dihedral_angle_4_deg 13.91 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 6.804 r_long_range_B_refined 3.109 r_long_range_B_other 3.107 r_scangle_other 1.915 r_mcangle_it 1.633 r_mcangle_other 1.633 r_angle_refined_deg 1.597
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.656 r_dihedral_angle_4_deg 13.91 r_dihedral_angle_3_deg 13.832 r_dihedral_angle_1_deg 6.804 r_long_range_B_refined 3.109 r_long_range_B_other 3.107 r_scangle_other 1.915 r_mcangle_it 1.633 r_mcangle_other 1.633 r_angle_refined_deg 1.597 r_scbond_it 1.154 r_scbond_other 1.154 r_angle_other_deg 1.002 r_mcbond_it 0.983 r_mcbond_other 0.983 r_chiral_restr 0.103 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 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 10401 Nucleic Acid Atoms Solvent Atoms 373 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing