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Cysteine Synthase from Trypanosoma cruzi with PLP and OAS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AIR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 Ammonium Sulfate, Bis-Tis
Crystal Properties Matthews coefficient Solvent content 2.26 45.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.006 α = 90 b = 66.667 β = 90.468 c = 167.518 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 PIXEL DECTRIS EIGER2 XE 16M 2020-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9762 Diamond I03
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 1.8 54.94 98.27 0.9961 12.93 3.37 110107
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 1.8 1.83 0.9059
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4AIR 1.8 54.94 110107 5483 97.867 0.193 0.1913 0.1908 0.2173 0.2168 24.233
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] -0.554 -0.123 0.046 0.51
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.063 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_2_deg 11.185 r_lrange_it 6.025 r_lrange_other 6.025 r_dihedral_angle_1_deg 5.782 r_scangle_it 4.293 r_scangle_other 4.293 r_mcangle_it 3.141 r_mcangle_other 3.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.063 r_dihedral_angle_3_deg 13.507 r_dihedral_angle_2_deg 11.185 r_lrange_it 6.025 r_lrange_other 6.025 r_dihedral_angle_1_deg 5.782 r_scangle_it 4.293 r_scangle_other 4.293 r_mcangle_it 3.141 r_mcangle_other 3.141 r_scbond_it 2.942 r_scbond_other 2.942 r_mcbond_it 2.273 r_mcbond_other 2.271 r_angle_refined_deg 1.362 r_angle_other_deg 0.468 r_symmetry_xyhbond_nbd_refined 0.264 r_symmetry_nbd_refined 0.261 r_nbd_refined 0.213 r_nbd_other 0.212 r_xyhbond_nbd_refined 0.203 r_symmetry_nbd_other 0.19 r_nbtor_refined 0.173 r_ncsr_local_group_1 0.103 r_ncsr_local_group_6 0.103 r_ncsr_local_group_3 0.101 r_ncsr_local_group_4 0.1 r_symmetry_nbtor_other 0.076 r_ncsr_local_group_5 0.076 r_chiral_restr 0.072 r_ncsr_local_group_2 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9335 Nucleic Acid Atoms Solvent Atoms 548 Heterogen Atoms 92
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing