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Cystathionine gamma-lyase N360S mutant from Toxoplasma gondii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NMP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291 12% (w/v) PEG 3350
0.1M sodium citrate pH 4.6
CYMAL-4
Crystal Properties Matthews coefficient Solvent content 3.65 66.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 157.738 α = 90 b = 157.738 β = 90 c = 93.331 γ = 120
Symmetry Space Group P 3 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 100 PIXEL DECTRIS PILATUS 6M 2021-01-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC 0.9792 ALBA XALOC
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 2.22 93.331 100 0.997 12.9 30 65911
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.22 2.26 0.888
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 2NMP 2.22 93.331 62550 3350 99.95 0.19558 0.19451 0.1962 0.21605 0.2132 RANDOM 24.852
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] -0.18 -0.09 -0.18 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 15.501 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 3.858 r_long_range_B_other 3.827 r_mcangle_it 1.639 r_mcangle_other 1.639 r_scangle_other 1.312 r_angle_refined_deg 1.189
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.943 r_dihedral_angle_4_deg 15.501 r_dihedral_angle_3_deg 13.73 r_dihedral_angle_1_deg 6.208 r_long_range_B_refined 3.858 r_long_range_B_other 3.827 r_mcangle_it 1.639 r_mcangle_other 1.639 r_scangle_other 1.312 r_angle_refined_deg 1.189 r_angle_other_deg 1.124 r_mcbond_it 0.894 r_mcbond_other 0.894 r_scbond_it 0.739 r_scbond_other 0.739 r_chiral_restr 0.044 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6109 Nucleic Acid Atoms Solvent Atoms 249 Heterogen Atoms 42
Software Software Software Name Purpose Aimless data scaling XDS data reduction PHENIX refinement PHASER phasing