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Crystal structure of O-Acetyl Serine Sulfhydrylase from Leishmania donovani in complex with designed tetrapeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SPX PDB ENTRY 3SPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 289 KSCN, PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.13 42.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.3 α = 90 b = 61.93 β = 90 c = 43.44 γ = 90
Symmetry Space Group P 21 21 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 MARMOSAIC 225 mm CCD 2010-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.77 50 97.9 0.074 9.9 6.9 29549 5.6 30.15
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 1.772 1.818 77.4 0.426 4
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 3SPX 1.77 34.69 29394 1527 99.63 0.17839 0.17686 0.177 0.20815 0.1942 RANDOM 20.637
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] -0.6 -0.64 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_4_deg 20.914 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 6.619 r_scangle_it 6.534 r_scbond_it 4.144 r_mcangle_it 2.463 r_angle_refined_deg 2.325 r_mcbond_it 1.503 r_chiral_restr 0.192
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.064 r_dihedral_angle_4_deg 20.914 r_dihedral_angle_3_deg 15.387 r_dihedral_angle_1_deg 6.619 r_scangle_it 6.534 r_scbond_it 4.144 r_mcangle_it 2.463 r_angle_refined_deg 2.325 r_mcbond_it 1.503 r_chiral_restr 0.192 r_bond_refined_d 0.03 r_gen_planes_refined 0.014 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2427 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data collection