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Crystal structure of O-succinylhomoserine sulfhydrylase from Mycobacterium tuberculosis covalently bound to pyridoxal-5-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1Y4I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 289 26.9 mg/mL protein against JCSG+ condition A2, 25% PEG 3000, 0.1 M citrate pH 5.5, crystal tracking ID 215797a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.58 52.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.95 α = 90 b = 129.56 β = 115.35 c = 95.96 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 ADSC QUANTUM 315r 2010-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
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 1.85 50 99.4 0.062 13.56 4.4 154137 153275 -3 33.417
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 1.85 1.9 99.6 0.529 2.5 4.2
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 1y4i 1.85 19.7 153169 7681 99.54 0.189 0.187 0.2016 0.223 0.2343 RANDOM 39.709
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] -2.02 -1.07 1.56 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.572 r_dihedral_angle_4_deg 15.248 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 5.271 r_scangle_it 2.529 r_scbond_it 1.512 r_angle_refined_deg 1.322 r_mcangle_it 0.953 r_mcbond_it 0.525 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.572 r_dihedral_angle_4_deg 15.248 r_dihedral_angle_3_deg 13.037 r_dihedral_angle_1_deg 5.271 r_scangle_it 2.529 r_scbond_it 1.512 r_angle_refined_deg 1.322 r_mcangle_it 0.953 r_mcbond_it 0.525 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12027 Nucleic Acid Atoms Solvent Atoms 1046 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction