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Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) from Fusobacterium nucleatum
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O58 PDB ENTRY 1O58
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 4% (w/v) PEG 8000, 0.1M Hepes pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.3 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.793 α = 90 b = 58.793 β = 90 c = 205.053 γ = 90
Symmetry Space Group P 43 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 95 CCD ADSC QUANTUM 210r 2011-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 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 2.9 33.64 98.5 0.137 17.4 3.8 8510
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 2.9 2.95 98.6 0.3 8.5 3.8
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 PDB ENTRY 1O58 2.91 33.64 8058 392 98.4 0.17502 0.17081 0.1747 0.26555 0.2646 RANDOM 22.987
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] -0.14 -0.14 0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.85 r_dihedral_angle_4_deg 25.827 r_dihedral_angle_3_deg 20.763 r_dihedral_angle_1_deg 8.118 r_angle_refined_deg 2.15 r_angle_other_deg 0.955 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.85 r_dihedral_angle_4_deg 25.827 r_dihedral_angle_3_deg 20.763 r_dihedral_angle_1_deg 8.118 r_angle_refined_deg 2.15 r_angle_other_deg 0.955 r_chiral_restr 0.11 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2599 Nucleic Acid Atoms Solvent Atoms 9 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing