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Crystal structure of 3-Mercaptopyruvate Sulfurtransferase(3MST) in complex with compound1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 PEG 3,350, HEPES-NaOH, NaCl
Crystal Properties Matthews coefficient Solvent content 2.17 43.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.355 α = 90 b = 150.36 β = 110.09 c = 54.307 γ = 90
Symmetry Space Group P 1 21 1
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 RAYONIX MX300HE 2014-10-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU
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 1.2 50 97.5 0.073 14.5 3.7 170429
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.2 1.22 100 0.736 0.59 3.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1.2 30.26 161958 8342 97.4 0.14117 0.1397 0.1467 0.17074 0.1752 RANDOM 13.309
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] 2.38 1.07 0.66 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.827 r_sphericity_free 17.115 r_dihedral_angle_4_deg 16.577 r_dihedral_angle_3_deg 12.766 r_sphericity_bonded 10.697 r_dihedral_angle_1_deg 5.941 r_scangle_other 3.781 r_long_range_B_refined 3.422 r_long_range_B_other 3.421 r_rigid_bond_restr 3.242
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.827 r_sphericity_free 17.115 r_dihedral_angle_4_deg 16.577 r_dihedral_angle_3_deg 12.766 r_sphericity_bonded 10.697 r_dihedral_angle_1_deg 5.941 r_scangle_other 3.781 r_long_range_B_refined 3.422 r_long_range_B_other 3.421 r_rigid_bond_restr 3.242 r_scbond_it 3.167 r_scbond_other 3.167 r_mcangle_it 2.343 r_mcangle_other 2.343 r_mcbond_it 2.016 r_mcbond_other 2.013 r_angle_refined_deg 1.85 r_angle_other_deg 0.887 r_chiral_restr 0.115 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4574 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing