☰ Navigation Tabs
Promiscuous amino acid gamma synthase from Caldicellulosiruptor hydrothermalis in closed conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold E4QC33
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 Well solution of 100 mM MES buffer, pH 6.5, 4-5% w/v gamma-PGA (Na+ form, low molecular weight), 12-15% w/v PEG 4000. Well solution was mixed in a 1:1 ratio with Cahy protein at 20 mg/mL
Crystal Properties Matthews coefficient Solvent content 2.77 55.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 279.09 α = 90 b = 133.12 β = 94.866 c = 115.79 γ = 90
Symmetry Space Group C 1 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 CCD RAYONIX MX300-HS 2022-10-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 1.1165 APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.7 40 97.1 0.107 0.999 15.1 14 446747
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.75 93.7 2.022 0.794 1.79 14.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.702 39.925 446714 22101 97.171 0.155 0.1539 0.1591 0.1791 0.1816 30.765
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] 0.116 -0.663 -0.099 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 13.947 r_dihedral_angle_3_deg 13.447 r_dihedral_angle_1_deg 7.547 r_lrange_it 5.699 r_lrange_other 5.662 r_scangle_it 3.653 r_scangle_other 3.653 r_scbond_it 2.451 r_scbond_other 2.451
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.477 r_dihedral_angle_4_deg 13.947 r_dihedral_angle_3_deg 13.447 r_dihedral_angle_1_deg 7.547 r_lrange_it 5.699 r_lrange_other 5.662 r_scangle_it 3.653 r_scangle_other 3.653 r_scbond_it 2.451 r_scbond_other 2.451 r_angle_refined_deg 1.944 r_mcangle_it 1.759 r_mcangle_other 1.759 r_angle_other_deg 1.695 r_mcbond_it 1.343 r_mcbond_other 1.343 r_nbd_other 0.238 r_nbd_refined 0.225 r_symmetry_nbd_other 0.211 r_nbtor_refined 0.21 r_symmetry_nbd_refined 0.198 r_xyhbond_nbd_refined 0.158 r_metal_ion_refined 0.153 r_symmetry_xyhbond_nbd_refined 0.146 r_symmetry_nbtor_other 0.094 r_chiral_restr 0.087 r_symmetry_xyhbond_nbd_other 0.083 r_bond_refined_d 0.021 r_gen_planes_refined 0.015 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26400 Nucleic Acid Atoms Solvent Atoms 2021 Heterogen Atoms 173
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing