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Crystal structure of hydrogen sulfide-producing enzyme (Fn1055) D232N mutant in complexed with alpha-aminoacrylate intermediate: lysine-dimethylated form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B53
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 24% (w/v) PEG3350, 0.1M Hepes pH 7.5, 0.2M Magnesium chloride hexahydrate
Crystal Properties Matthews coefficient Solvent content 3.3 63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 191.046 α = 90 b = 57.127 β = 100.89 c = 94.293 γ = 90
Symmetry Space Group C 1 2 1
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 2011-11-30 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 2.14 60.43 95.6 0.066 20.8 7.6 52807
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 2.14 2.2 95.3 0.25 7.3 7.7
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 5B53 2.14 36.66 50143 2648 95.11 0.20288 0.20106 0.2076 0.2371 0.2454 RANDOM 24.482
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] 2.51 -1.44 -0.79 -1.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 17.124 r_dihedral_angle_3_deg 15.988 r_dihedral_angle_1_deg 6.479 r_long_range_B_refined 6.273 r_long_range_B_other 6.198 r_scangle_other 4.675 r_mcangle_it 3.068 r_mcangle_other 3.068 r_scbond_it 2.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.032 r_dihedral_angle_4_deg 17.124 r_dihedral_angle_3_deg 15.988 r_dihedral_angle_1_deg 6.479 r_long_range_B_refined 6.273 r_long_range_B_other 6.198 r_scangle_other 4.675 r_mcangle_it 3.068 r_mcangle_other 3.068 r_scbond_it 2.966 r_scbond_other 2.963 r_mcbond_other 2.109 r_mcbond_it 2.108 r_angle_refined_deg 1.851 r_angle_other_deg 1.36 r_chiral_restr 0.278 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.007 r_gen_planes_other 0.006 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 5241 Nucleic Acid Atoms Solvent Atoms 319 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing