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Crystal structure of cysteine synthase A from Limosilactobacillus reuteri LR1 in its apo form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5XOQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 288 0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% PEG6000
Crystal Properties Matthews coefficient Solvent content 2.48 50.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.642 α = 90 b = 101.292 β = 107.33 c = 63.53 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 RIGAKU HyPix-6000HE 2024-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.2 20.4 98.9 0.273 0.308 0.139 0.973 5.4 4.8 32499
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.27 98.1 1.331 1.489 0.657 0.412 5
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 5XOQ 2.2 20.4 30892 1583 98.65 0.21452 0.21156 0.2116 0.27136 0.2714 RANDOM 33.791
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] 0.77 0.26 -0.64 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.812 r_long_range_B_refined 11.366 r_dihedral_angle_1_deg 8.112 r_mcangle_it 7.57 r_dihedral_angle_2_deg 6.951 r_scbond_it 6.628 r_mcbond_it 5.315 r_angle_refined_deg 2.937 r_chiral_restr 0.246 r_bond_refined_d 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.812 r_long_range_B_refined 11.366 r_dihedral_angle_1_deg 8.112 r_mcangle_it 7.57 r_dihedral_angle_2_deg 6.951 r_scbond_it 6.628 r_mcbond_it 5.315 r_angle_refined_deg 2.937 r_chiral_restr 0.246 r_bond_refined_d 0.015 r_gen_planes_refined 0.012 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3953 Nucleic Acid Atoms Solvent Atoms 86 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement Aimless data scaling CrysalisPro data reduction MOLREP phasing PDB_EXTRACT data extraction