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Promiscuous amino acid gamma synthase from Caldicellulosiruptor hydrothermalis in open 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 293 16% PEG 3350, 0.125 M Sodium Thiocyanate pH 8.0. Protein was 20 mg/mL in 50 mM HEPES pH 7.5. Four microliter drops were formed with a 1:1 mixture of protein and well solution. Crystals formed slowly over the course of 10 months
Crystal Properties Matthews coefficient Solvent content 2.37 48.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.921 α = 90 b = 79.921 β = 90 c = 230.492 γ = 120
Symmetry Space Group P 31 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 MX-300 2022-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97856 APS 21-ID-G
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 2.3 45 99.9 0.126 0.999 13.6 10.7 38922
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.36 99.8 1.949 0.473 1.29 9.2
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.3 44.324 38898 2006 99.915 0.209 0.2073 0.243 0.2207 58.219
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] 0.698 0.349 0.698 -2.264
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 16.27 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_1_deg 6.71 r_lrange_it 2.95 r_lrange_other 2.949 r_scangle_it 1.702 r_scangle_other 1.702 r_mcangle_it 1.561 r_mcangle_other 1.561
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.508 r_dihedral_angle_4_deg 16.27 r_dihedral_angle_3_deg 14.486 r_dihedral_angle_1_deg 6.71 r_lrange_it 2.95 r_lrange_other 2.949 r_scangle_it 1.702 r_scangle_other 1.702 r_mcangle_it 1.561 r_mcangle_other 1.561 r_angle_refined_deg 1.305 r_angle_other_deg 1.165 r_scbond_it 1.032 r_scbond_other 1.032 r_mcbond_it 0.957 r_mcbond_other 0.957 r_nbd_refined 0.181 r_nbd_other 0.179 r_symmetry_nbd_refined 0.174 r_symmetry_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.157 r_xyhbond_nbd_refined 0.144 r_symmetry_nbtor_other 0.076 r_chiral_restr 0.05 r_bond_refined_d 0.004 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6149 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing